Fixed stdout output

versions of python

LICENSE

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+
+  CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+Version 2.1 dated 2013-06-21
+
+
+    Notice
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+
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+
+
+    Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
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+jurisdiction, by the more diligent Party.

MANIFEST.in

@@ -1,11 +1,12 @@
 include setup.py
-recursive-include distutils.ext *.py *.c *.pem
-recursive-include python *.pyx *.pxd *.c *.h *.cfiles
+recursive-include python *.pyx *.pxd *.c *.h
 recursive-include src *.c *.h
+include src/CMakeLists.txt
 recursive-include doc/sphinx/source *.txt *.rst *.py
 recursive-include doc/sphinx/sphinxext *.py
 include doc/sphinx/Makefile
 include doc/sphinx/Doxyfile
-include README.txt
+include README.md
 include requirements.txt
+include scripts/obi
 

README.md

@@ -0,0 +1,41 @@
+The `OBITools3`: A package for the management of analyses and data in DNA metabarcoding   
+---------------------------------------------
+
+**Website: <https://metabarcoding.org/obitools3>**
+
+DNA metabarcoding offers new perspectives for biodiversity research [1]. This approach of ecosystem studies relies heavily on the use of Next-Generation Sequencing (NGS), and consequently requires the ability to to treat large volumes of data. The `OBITools` package  satisfies this requirement thanks to a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context [2] - <https://metabarcoding.org/obitools>. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to setup tailored-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.   
+
+
+
+**The `OBITools3`.** This new version of the `OBITools` looks to significantly improve the storage efficiency and the data processing speed. To this end, the `OBITools3` rely on an ad hoc database system, inside which all the data that a DNA metabarcoding experiment must consider is stored: the sequences, the metadata (describing for instance the samples), the database containing the reference sequences used for the taxonomic annotation, as well as the taxonomic databases. Besides the gain in efficiency, this new structure allows an easier access to all the data associated with an experiment.   
+
+
+
+**Column-oriented storage.** An analysis pipeline corresponds to a succession of commands, each computing one step of the analysis, and where the result of the command *n* is used by the command *n+1*. DNA metabarcoding data can easily be represented in the form of tables, and each command can be regarded as an operation transforming one or several 'input' tables into one or several 'output' tables, which can be used by the next command. Many of the basic operations in a pipeline copy without modification an important part of the input tables to the result tables, and use for their calculations only a small part of the input data. In the original `OBITools`, those tables are kept in the form of annotated sequence files in the FASTA or FASTQ format. This has two consequences: i) keeping the transitional results of the analysis pipeline means using disk space for an important volume of redundant data, ii) The coding and decoding of informations that are not actually used represent an important part of the treatment process. The new database system used by the `OBITools3` (called DMS for Data Management System) relies on column-oriented storage. The columns are immutable and can be assembled in views representing the data tables. This way, the data not modified by a command in an input table can easily be associated to the result table without duplicating any information ; and the data not used at all by a command can be associated with the result table without being read. This strategy results in a gain in disk space efficiency by limiting data redundancy, as well as a gain in execution time by limiting data reading, writing and conversion operations. Finally, as a mean to optimize data access, each column is stored in a binary file directly mapped in memory for reading and writing operations.   
+
+
+
+**Storage optimization.** DNA metabarcoding data is intrinsically very redundant. For example, the same sequence corresponding to a species will be present several thousand times across all samples. In order to limit the disk space used and make comparison operations more efficient, data in the form of character strings is stored in columns using a complex indexing structure, efficient on millions of values, coupling hash functions, Bloom filters and AVL trees. Finally, DNA sequences are compressed by encoding each nucleotide on two or four bits depending on whether the sequences contain only the four nucleotides (A, C, G, T) or use the IUPAC codes.   
+
+
+
+**Saving the data processing history.** The totality of the informations used by the `OBITools3` is stored in immutable data structures in the DMS. If a command has to modify a column used as input to produce its result, a new version of that column is created, leaving the initial version intact. This storage system enables to keep, at minimal cost, the totality of the transitional results produced by the pipeline. The storage of metadata describing all the operations that have produced a view (a result table) in the DMS makes possible the creation of an oriented hypergraph, where each node corresponds to a view and each arrow to an operation. By retracing the dependency relationships in this hypergraph, it is possible to rebuild *a posteriori* the entirety of the process that has produced a result table.   
+
+
+
+**Tools.** The `OBITools3` offer the same tools as the original `OBITools`, plus `ecoPCR` (*in silico* PCR) [4] and `Sumatra` (sequence alignment, not multithreaded yet) [5]. 
+Eventually, new versions of `ecoPrimers` (PCR primer design) [3], as well as `Sumaclust` (sequence alignment and clustering) [5] will be added, taking advantage of the database structure developed for the `OBITools3`.    
+
+
+
+**Implementation and disponibility.** The lower layers managing the DMS as well as all the compute-intensive functions are coded in `C99` for efficiency reasons. A `Cython` (<http://www.cython.org>) object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3`. The `OBITools3` are now being released, check the wiki for more information.
+
+
+
+**References.**
+
+1. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH: Environmental DNA. Mol Ecol 2012:1789–1793.
+2. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E: OBITools: a Unix-inspired software package for DNA metabarcoding. Mol Ecol Resour, 2016: 176-182.
+3. Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E: ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res 2011, 39:e145.
+4. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, Taberlet P, Pompanon F: An in silico approach for the evaluation of DNA barcodes. BMC Genomics 2010, 11:434.
+5. Mercier C, Boyer F, Bonin A, Coissac E (2013) SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Available: <http://metabarcoding.org/sumatra> and <http://metabarcoding.org/sumaclust>

c-sandbox/obicount/Makefile

@@ -1,18 +0,0 @@
-CC = gcc
-CFLAGS = -c -Wall
-LDFLAGS = 
-SOURCES = obicount.c ../obidmscolumn.c
-OBJECTS = $(SOURCES:.c=.o)
-EXECUTABLE = obicount
-
-all: $(SOURCES) $(EXECUTABLE)
-    
-$(EXECUTABLE): $(OBJECTS) 
-	$(CC) $(LDFLAGS) $(OBJECTS) -o $@
-
-.c.o:
-	$(CC) $(CFLAGS) $< -o $@
-
-clean:
-	rm *o
-	rm $(EXECUTABLE)

c-sandbox/obicount/obicount.c

@@ -1,87 +0,0 @@
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <sys/mman.h>	/* mmap() is defined in this header */
-#include <stdint.h>
-#include <fcntl.h>
-#include <sys/stat.h>
-
-#include "../obitypes.h"
-#include "../obidmscolumn.h"
-
-
-/**
- * @brief Computes the size to map.
- *
- * * @param OBIDMSColumn_file The file to map.
- * @return The size to map.
- */
-int get_size_to_map(int OBIDMSColumn_file)
-// compute size to map : file size minus size of the header
-{
-	int size;
-	struct stat s;
-
-	fstat(OBIDMSColumn_file, &s);
-	size = (s.st_size) - HEADER_SIZE;
-	return(size);
-}
-
-/**
- * @brief Computes and prints the total number of sequences by summing their counts.
- *
- * * @param The count file.
- */
-int main(int argc, char const *argv[])
-{
-	char* map;
-	int size;
-	int OBIDMSColumn_file;
-	int count;
-	char c;
-	char num_str[10] = "";
-	int num_int;
-	int i,j;
-
-	// initialize variables
-	OBIDMSColumn_file = open(argv[1], O_RDONLY);	//read only
-	count = 0;
-	j = 0;
-
-	// compute size to map
-	size = get_size_to_map(OBIDMSColumn_file);
-
-	// map the data
-	map = obi_map_read_only(OBIDMSColumn_file, HEADER_SIZE, size);
-
-	// sum the counts
-	for (i=0; i<size; i++)
-	{
-		c = map[i];
-
-		if (c != SEPARATOR)		// reading lines
-		{
-			num_str[j] = c;
-			j++;
-		}
-
-		else if (c == SEPARATOR)	// end of a line
-		{
-			num_int = atoi(num_str);	// turn number from character string to int
-			count = count + num_int;	// add the number to the sum
-			j = 0;
-			num_str[j] = '\0';
-		}
-	}
-
-	// print the final count of sequences
-	fprintf(stderr, "Sequence count = %d\n", count);
-
-	// unmap
-	obi_unmap(size);
-
-	// close file
-	close(OBIDMSColumn_file);
-
-	return(0);
-}

distutils.ext/obidistutils/command/build.py

@@ -1,38 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-from distutils.command.build import build as ori_build
-from obidistutils.serenity.checksystem import is_mac_system
-
-
-class build(ori_build):
-    
-    def has_ext_modules(self):
-        return self.distribution.has_ext_modules()
-    
-    def has_pidname(self):
-        return is_mac_system()
-
-    def has_doc(self):
-        return True
-    
-    def has_littlebigman(self):
-        return True
-    
-    try:
-        from obidistutils.command.build_sphinx import build_sphinx  # @UnusedImport
-
-        sub_commands = [("littlebigman",has_littlebigman),
-                         ('pidname',has_pidname)
-                       ] \
-                       + ori_build.sub_commands + \
-                       [('build_sphinx',has_doc)]
-    except ImportError:
-        sub_commands = [("littlebigman",has_littlebigman),
-                         ('pidname',has_pidname)
-                       ] \
-                       + ori_build.sub_commands
-        

distutils.ext/obidistutils/command/build_cexe.py

@@ -1,85 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-from .build_ctools import build_ctools
-from .build_exe import build_exe
-from distutils.errors import DistutilsSetupError
-from distutils import log
-import os
-
-class build_cexe(build_ctools):
-
-    description = "build C/C++ executable distributed with Python extensions"
-
-
-    def initialize_options(self):
-        build_ctools.initialize_options(self)
-        self.built_files = None
-
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-
-        build_cexe_dir = self.build_cexe
-        build_ctools.finalize_options(self)
-
-        if build_cexe_dir is None:
-            self.build_cexe=None
-            
-        self.set_undefined_options('build',
-                                   ('build_scripts',  'build_cexe'))
-
-        self.set_undefined_options('build_files',
-                                   ('files',  'built_files'))
-                   
-        self.executables   = self.distribution.executables
-#         self.build_cexe = os.path.join(os.path.dirname(self.build_cexe),'cbinaries') 
-#         self.mkpath(self.build_cexe)
-
-        if self.executables:
-            self.check_executable_list(self.executables)
-                            
-
-        # XXX same as for build_ext -- what about 'self.define' and
-        # 'self.undef' ?
-
-    def substitute_sources(self,exe_name,sources):
-        """
-        Substitutes source file name starting by an @ by the actual
-        name of the built file (see --> build_files)
-        """
-        sources = list(sources)
-        for i in range(len(sources)):
-            message = "%s :-> %s" % (exe_name,sources[i])
-            if sources[i][0]=='@':
-                try:
-                    filename = self.built_files[sources[i][1:]]
-                except KeyError:
-                    raise DistutilsSetupError(
-                         'The %s filename declared in the source '
-                         'files of the program %s have not been '
-                         'built by the installation process' % (sources[i],
-                                                                exe_name))
-                sources[i]=filename
-                log.info("%s changed to %s",message,filename)
-            else:
-                log.info("%s ok",message)
-
-        return sources
- 
-    def run(self):
-
-        for cmd_name in self.get_sub_commands():
-            self.run_command(cmd_name)
-
-        build_exe.run(self)
-        
-
-   

distutils.ext/obidistutils/command/build_ctools.py

@@ -1,63 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-
-from .build_exe import build_exe
-from distutils import log
-
-class build_ctools(build_exe):
-    description = "build C/C++ executable not distributed with Python extensions"
-
-    def initialize_options(self):
-        build_exe.initialize_options(self)
-        
-        # List of built tools
-        self.ctools = None
-        self.littlebigman = None
-
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-            
-        build_exe.finalize_options(self)
-        
-        
-        self.set_undefined_options('build',
-                                    ('build_temp', 'build_cexe'))
-
-        self.set_undefined_options('littlebigman',
-                                   ('littlebigman',  'littlebigman'))
-                   
-        self.executables = self.distribution.ctools
-        self.check_executable_list(self.executables)
-        
-
-        if self.littlebigman =='-DLITTLE_END':
-            if self.define is None:
-                self.define=[('LITTLE_END',None)]
-            else:
-                self.define.append('LITTLE_END',None)
-                
-        log.info('Look for CPU architecture... %s',self.define)
-
-        self.ctools = set()
-
-    def run(self):
-
-        for cmd_name in self.get_sub_commands():
-            self.run_command(cmd_name)
-
-        
-        build_exe.run(self)
-        
-        for e,p in self.executables:                                  # @UnusedVariable
-            self.ctools.add(e)
-            
-

distutils.ext/obidistutils/command/build_exe.py

@@ -1,211 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os
-
-from distutils.core import Command
-from distutils.sysconfig import customize_compiler
-from distutils.errors import DistutilsSetupError
-from distutils import log
-from distutils.ccompiler import show_compilers
-
-class build_exe(Command):
-    
-    description = "build an executable -- Abstract command "
-
-    user_options = [
-        ('build-cexe', 'x',
-         "directory to build C/C++ libraries to"),
-        ('build-temp', 't',
-         "directory to put temporary build by-products"),
-        ('debug', 'g',
-         "compile with debugging information"),
-        ('force', 'f',
-         "forcibly build everything (ignore file timestamps)"),
-        ('compiler=', 'c',
-         "specify the compiler type"),
-        ]
-
-    boolean_options = ['debug', 'force']
-
-    help_options = [
-        ('help-compiler', None,
-         "list available compilers", show_compilers),
-        ]
-
-    def initialize_options(self):
-        self.build_cexe = None
-        self.build_temp = None
-
-        # List of executables to build
-        self.executables = None
-
-        # Compilation options for all libraries
-        self.include_dirs = None
-        self.define = None
-        self.undef = None
-        self.extra_compile_args = None
-        self.debug = None
-        self.force = 0
-        self.compiler = None
-        self.sse = None
-        self.built_files=None
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-        self.set_undefined_options('build',
-                                   ('build_temp', 'build_temp'),
-                                   ('compiler', 'compiler'),
-                                   ('debug', 'debug'),
-                                   ('force', 'force'))
-
-        if self.include_dirs is None:
-            self.include_dirs = self.distribution.include_dirs or []
-            
-        if isinstance(self.include_dirs, str):
-            self.include_dirs = self.include_dirs.split(os.pathsep)
-
-        self.sse = self.distribution.sse
-        
-        if self.sse is not None:
-            if self.extra_compile_args is None:
-                self.extra_compile_args=['-m%s' % self.sse]
-            else:
-                self.extra_compile_args.append('-m%s' % self.sse)
-
-        # XXX same as for build_ext -- what about 'self.define' and
-        # 'self.undef' ?
-
-    def run(self):
-
-        if not self.executables:
-            return
-
-        self.mkpath(self.build_cexe)
-
-        # Yech -- this is cut 'n pasted from build_ext.py!
-        from distutils.ccompiler import new_compiler
-        self.compiler = new_compiler(compiler=self.compiler,
-                                     dry_run=self.dry_run,
-                                     force=self.force)
-        customize_compiler(self.compiler)
-
-        if self.include_dirs is not None:
-            self.compiler.set_include_dirs(self.include_dirs)
-        if self.define is not None:
-            # 'define' option is a list of (name,value) tuples
-            for (name,value) in self.define:
-                self.compiler.define_macro(name, value)
-
-        if self.undef is not None:
-            for macro in self.undef:
-                self.compiler.undefine_macro(macro)
-                
-        self.build_executables(self.executables)
-
-
-    def check_executable_list(self, executables):
-        """Ensure that the list of executables is valid.
-
-        `executable` is presumably provided as a command option 'executables'.
-        This method checks that it is a list of 2-tuples, where the tuples
-        are (executable_name, build_info_dict).
-
-        Raise DistutilsSetupError if the structure is invalid anywhere;
-        just returns otherwise.
-        """
-        if not isinstance(executables, list):
-            raise DistutilsSetupError("'executables' option must be a list of tuples")
-
-        for exe in executables:
-            if not isinstance(exe, tuple) and len(exe) != 2:
-                raise DistutilsSetupError("each element of 'executables' must a 2-tuple")
-
-            name, build_info = exe
-
-            if not isinstance(name, str):
-                raise DistutilsSetupError(
-                      "first element of each tuple in 'executables' " 
-                      "must be a string (the executables name)")
-                
-            if '/' in name or (os.sep != '/' and os.sep in name):
-                raise DistutilsSetupError(
-                       "bad executable name '%s': " 
-                       "may not contain directory separators" % exe[0])
-
-            if not isinstance(build_info, dict):
-                raise DistutilsSetupError(
-                      "second element of each tuple in 'executables' " 
-                      "must be a dictionary (build info)")
-
-    def get_executable_names(self):
-        # Assume the executables list is valid -- 'check_executable_list()' is
-        # called from 'finalize_options()', so it should be!
-        if not self.executables:
-            return None
-
-        exe_names = []
-        for (exe_name, build_info) in self.executables:                     # @UnusedVariable
-            exe_names.append(exe_name)
-        return exe_names
-
-
-    def get_source_files(self):
-        self.check_executable_list(self.executables)
-        filenames = []
-        for (exe_name, build_info) in self.executables:                     # @UnusedVariable
-            sources = build_info.get('sources')
-            if sources is None or not isinstance(sources, (list, tuple)):
-                raise DistutilsSetupError(
-                       "in 'executables' option (library '%s'), "
-                       "'sources' must be present and must be "
-                       "a list of source filenames" % exe_name)
-
-            filenames.extend(sources)
-        return filenames
-    
-    def substitute_sources(self,exe_name,sources):
-        return list(sources)
-
-    def build_executables(self, executables):
-        for (exe_name, build_info) in executables:
-            sources = build_info.get('sources')
-            if sources is None or not isinstance(sources, (list, tuple)):
-                raise DistutilsSetupError(
-                       "in 'executables' option (library '%s'), " 
-                       "'sources' must be present and must be " 
-                       "a list of source filenames" % exe_name)
-                
-            sources = self.substitute_sources(exe_name,sources)
-
-            log.info("building '%s' program", exe_name)
-
-            # First, compile the source code to object files in the library
-            # directory.  (This should probably change to putting object
-            # files in a temporary build directory.)
-            macros = build_info.get('macros')
-            include_dirs = build_info.get('include_dirs')
-            extra_args = self.extra_compile_args or []
-            
-            objects = self.compiler.compile(sources,
-                                            output_dir=self.build_temp,
-                                            macros=macros,
-                                            include_dirs=include_dirs,
-                                            extra_postargs=extra_args,
-                                            debug=self.debug)
-
-            # Now "link" the object files together into a static library.
-            # (On Unix at least, this isn't really linking -- it just
-            # builds an archive.  Whatever.)
-            self.compiler.link_executable(objects, exe_name,
-                                            output_dir=self.build_cexe,
-                                            debug=self.debug)
-
-        

distutils.ext/obidistutils/command/build_ext.py

@@ -1,113 +0,0 @@
-'''
-Created on 13 fevr. 2014
-
-@author: coissac
-'''
-
-from distutils import log
-import os
-
-from Cython.Distutils import build_ext  as ori_build_ext  # @UnresolvedImport
-
-from Cython.Compiler import Options as cython_options  # @UnresolvedImport
-
-from distutils.errors import DistutilsSetupError
-
-class build_ext(ori_build_ext):
-
-    
-    def modifyDocScripts(self):
-        build_dir_file=open("doc/sphinx/build_dir.txt","w")
-        print(self.build_lib,file=build_dir_file)
-        build_dir_file.close()
-        
-    def initialize_options(self):
-        ori_build_ext.initialize_options(self)  # @UndefinedVariable
-        self.littlebigman = None
-        self.built_files = None
-
-    
-    def finalize_options(self):
-        ori_build_ext.finalize_options(self)  # @UndefinedVariable
-
-        self.set_undefined_options('littlebigman',
-                                   ('littlebigman',  'littlebigman'))
-        
-        self.set_undefined_options('build_files',
-                                   ('files',  'built_files'))
-
-        self.cython_c_in_temp = 1
-                   
-        if self.littlebigman =='-DLITTLE_END':
-            if self.define is None:
-                self.define=[('LITTLE_END',None)]
-            else:
-                self.define.append('LITTLE_END',None)
-        
-    def substitute_sources(self,exe_name,sources):
-        """
-        Substitutes source file name starting by an @ by the actual
-        name of the built file (see --> build_files)
-        """
-        sources = list(sources)
-        for i in range(len(sources)):
-            message = "%s :-> %s" % (exe_name,sources[i])
-            if sources[i][0]=='@':
-                try:
-                    filename = self.built_files[sources[i][1:]]
-                except KeyError:
-                    tmpfilename = os.path.join(self.build_temp,sources[i][1:])
-                    if os.path.isfile       (tmpfilename):
-                        filename = tmpfilename
-                    else:
-                        raise DistutilsSetupError(
-                             'The %s filename declared in the source '
-                             'files of the program %s have not been '
-                             'built by the installation process' % (sources[i],
-                                                                     exe_name))
-                sources[i]=filename
-                log.info("%s changed to %s",message,filename)
-            else:
-                log.info("%s ok",message)
-
-        return sources
-
-    def build_extensions(self):
-        # First, sanity-check the 'extensions' list
-        
-        for ext in self.extensions:
-            ext.sources = self.substitute_sources(ext.name,ext.sources)
-            
-        self.check_extensions_list(self.extensions)
-
-        for ext in self.extensions:
-            log.info("%s :-> %s",ext.name,ext.sources)
-            ext.sources = self.cython_sources(ext.sources, ext)
-            self.build_extension(ext)
-
-        
-    def run(self):
-        self.modifyDocScripts()
-
-        for cmd_name in self.get_sub_commands():
-            self.run_command(cmd_name)
-
-        cython_options.annotate = True
-        ori_build_ext.run(self)  # @UndefinedVariable
-        
-
-    def has_files(self):
-        return self.distribution.has_files()
-
-    def has_executables(self):
-        return self.distribution.has_executables()
-    
-    sub_commands = [('build_files',has_files),
-                    ('build_cexe', has_executables)
-                    ] + \
-                   ori_build_ext.sub_commands
-
-        
-
-
-        

distutils.ext/obidistutils/command/build_files.py

@@ -1,63 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os.path
-
-from distutils.core import Command
-from distutils import log
-
-class build_files(Command):
-            
-    def initialize_options(self):
-        self.files=None
-        self.ctools=None
-        self.build_temp=None
-        self.build_cexe=None
-
-    def finalize_options(self):
-        
-        self.set_undefined_options('build_ctools',
-                                   ('ctools',  'ctools'),
-                                   ('build_temp','build_temp'),
-                                   ('build_cexe','build_cexe'),
-                                   )
-        
-        self.files = {}
-        
-    def run(self):
-
-        for cmd_name in self.get_sub_commands():
-            self.run_command(cmd_name)
-
-        
-        for dest,prog,command in self.distribution.files:
-            destfile = os.path.join(self.build_temp,dest)
-            if prog in self.ctools:
-                progfile = os.path.join(self.build_cexe,prog)
-            else:
-                progfile = prog 
-                
-            log.info("Building file : %s" % dest)
-            
-            commandline = command % {'prog' : progfile,
-                                     'dest' : destfile}
-
-            log.info("    --> %s" % commandline)
-            
-            os.system(commandline)
-            self.files[dest]=destfile
-            
-            log.info("Done.\n")
-            
-    def has_ctools(self):
-        return self.distribution.has_ctools()
-
-
-    sub_commands = [('build_ctools', has_ctools)] + \
-                   Command.sub_commands
-            
-            
-        

distutils.ext/obidistutils/command/build_scripts.py

@@ -1,104 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os.path
-
-from distutils.command.build_scripts import build_scripts as ori_build_scripts
-from distutils.util import convert_path
-from distutils import log, sysconfig
-from distutils.dep_util import newer
-from stat import ST_MODE
-import re
-
-first_line_re = re.compile('^#!.*python[0-9.]*([ \t].*)?$')
-
-class build_scripts(ori_build_scripts):
-            
-    def copy_scripts (self):
-        """Copy each script listed in 'self.scripts'; if it's marked as a
-        Python script in the Unix way (first line matches 'first_line_re',
-        ie. starts with "\#!" and contains "python"), then adjust the first
-        line to refer to the current Python interpreter as we copy.
-        """        
-        self.mkpath(self.build_dir)
-        rawbuild_dir = os.path.join(os.path.dirname(self.build_dir),'raw_scripts')
-        self.mkpath(rawbuild_dir)
-        
-        outfiles = []
-        for script in self.scripts:
-            adjust = 0
-            script = convert_path(script)
-            outfile = os.path.join(self.build_dir, os.path.splitext(os.path.basename(script))[0])
-            rawoutfile = os.path.join(rawbuild_dir, os.path.basename(script))
-            outfiles.append(outfile)
-
-            if not self.force and not newer(script, outfile):
-                log.debug("not copying %s (up-to-date)", script)
-                continue
-
-            # Always open the file but ignore failures in dry-run mode --
-            # that way, we'll get accurate feedback if we can read the
-            # script.
-            try:
-                f = open(script, "r")
-            except IOError:
-                if not self.dry_run:
-                    raise
-                f = None
-            else:
-                first_line = f.readline()
-                if not first_line:
-                    self.warn("%s is an empty file (skipping)" % script)
-                    continue
-
-                match = first_line_re.match(first_line)
-                if match:
-                    adjust = 1
-                    post_interp = match.group(1) or ''
-            
-            log.info("Store the raw script %s -> %s", script,rawoutfile)        
-            self.copy_file(script, rawoutfile)
-
-
-            if adjust:
-                log.info("copying and adjusting %s -> %s", script,
-                         self.build_dir)
-                if not self.dry_run:
-                    outf = open(outfile, "w")
-                    if not sysconfig.python_build:
-                        outf.write("#!%s%s\n" %
-                                   (self.executable,
-                                    post_interp))
-                    else:
-                        outf.write("#!%s%s\n" %
-                                   (os.path.join(
-                            sysconfig.get_config_var("BINDIR"),
-                           "python%s%s" % (sysconfig.get_config_var("VERSION"),
-                                           sysconfig.get_config_var("EXE"))),
-                                    post_interp))
-                    outf.writelines(f.readlines())
-                    outf.close()
-                if f:
-                    f.close()
-            else:
-                if f:
-                    f.close()
-                self.copy_file(script, outfile)
-
-        if os.name == 'posix':
-            for F in outfiles:
-                if self.dry_run:
-                    log.info("changing mode of %s", F)
-                else:
-                    oldmode = os.stat(F)[ST_MODE]
-                    oldmode = oldmode & 0o7777
-                    
-                    newmode = (oldmode | 0o555) & 0o7777
-                    if newmode != oldmode:
-                        log.info("changing mode of %s from %o to %o",
-                                 F, oldmode, newmode)
-                        os.chmod(F, newmode)
-

distutils.ext/obidistutils/command/build_sphinx.py

@@ -1,27 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-
-try:
-    from sphinx.setup_command import BuildDoc as ori_build_sphinx  # @UnresolvedImport
-        
-    class build_sphinx(ori_build_sphinx):
-        '''Build Sphinx documentation in html, epub and man formats 
-        '''
-    
-        description = __doc__
-    
-        def run(self):
-            self.builder='html'
-            self.finalize_options()
-            ori_build_sphinx.run(self)
-            self.builder='epub'
-            self.finalize_options()
-            ori_build_sphinx.run(self)
-            self.builder='man'
-            self.finalize_options()
-            ori_build_sphinx.run(self)
-except ImportError:
-    pass  

distutils.ext/obidistutils/command/install.py

@@ -1,19 +0,0 @@
-'''
-Created on 6 oct. 2014
-
-@author: coissac
-'''
-
-# try:
-#     from setuptools.command.install import install as install_ori
-# except ImportError:
-#     from distutils.command.install import install as install_ori
-
-from distutils.command.install import install as install_ori
-
-class install(install_ori):
-    
-    def __init__(self,dist):
-        install_ori.__init__(self, dist)
-#        self.sub_commands.insert(0, ('build',lambda self: True))
-        self.sub_commands.append(('install_sphinx',lambda self: self.distribution.serenity))

distutils.ext/obidistutils/command/install_scripts.py

@@ -1,47 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-# try:
-#     from setuptools.command.install_scripts import install_scripts as ori_install_scripts
-# except ImportError:
-#     from distutils.command.install_scripts import install_scripts as ori_install_scripts
-
-from distutils.command.install_scripts import install_scripts as ori_install_scripts
-
-import os.path
-from distutils import log
-
-class install_scripts(ori_install_scripts):
-
-    def initialize_options(self):
-        ori_install_scripts.initialize_options(self)
-        self.public_dir = None
-                        
-                    
-    def install_public_link(self):
-        self.mkpath(self.public_dir)
-        for file in self.get_outputs():
-            log.info("exporting file %s -> %s", file,os.path.join(self.public_dir,
-                                    os.path.split(file)[1]
-                                    ))
-            if not self.dry_run:
-                dest = os.path.join(self.public_dir,
-                                    os.path.split(file)[1]
-                                   )
-                if os.path.exists(dest):
-                    os.unlink(dest)
-                os.symlink(file,dest)
-                    
-
-
-    def run(self):
-        ori_install_scripts.run(self)
-        if self.distribution.serenity:
-            self.public_dir=os.path.join(self.install_dir,"../export/bin")
-            self.public_dir=os.path.abspath(self.public_dir)
-            self.install_public_link()
-
-

distutils.ext/obidistutils/command/install_sphinx.py

@@ -1,61 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-from distutils.core import Command
-import os.path
-import glob
-
-class install_sphinx(Command):
-    '''
-    Install the sphinx documentation
-    '''
-    
-    description = "Install the sphinx documentation in serenity mode"
-
-    boolean_options = ['force', 'skip-build']
-
-
-    def initialize_options (self):
-        self.install_doc = None
-        self.build_dir = None
-
-    def finalize_options (self):
-        self.set_undefined_options('build_sphinx', ('build_dir', 'build_dir'))
-        self.set_undefined_options('install',
-                                   ('install_scripts', 'install_doc'))
-
-    def run (self):
-        if self.distribution.serenity:
-            self.install_doc = os.path.join(self.install_doc,"../export/share")
-            self.install_doc=os.path.abspath(self.install_doc)
-            self.mkpath(self.install_doc)
-            self.mkpath(os.path.join(self.install_doc,'html'))
-            outfiles = self.copy_tree(os.path.join(self.build_dir,'html'),  # @UnusedVariable
-                                      os.path.join(self.install_doc,'html'))
-                
-            self.mkpath(os.path.join(self.install_doc,'man','man1'))
-            outfiles = self.copy_tree(os.path.join(self.build_dir,'man'),  # @UnusedVariable
-                                      os.path.join(self.install_doc,'man','man1'))
-
-            for epub in glob.glob(os.path.join(self.build_dir,'epub/*.epub')):
-                self.copy_file(os.path.join(epub), 
-                               os.path.join(self.install_doc,os.path.split(epub)[1]))
-            
-    def get_outputs(self):
-        directory=os.path.join(self.install_doc,'html')
-        files = [os.path.join(self.install_doc,'html', f) 
-                 for dp, dn, filenames in os.walk(directory) for f in filenames]  # @UnusedVariable
-        
-        directory=os.path.join(self.build_dir,'man')
-        files.append(os.path.join(self.install_doc,'man','man1', f) 
-                 for dp, dn, filenames in os.walk(directory) for f in filenames)  # @UnusedVariable
-
-        directory=os.path.join(self.build_dir,'epub')
-        files.append(os.path.join(self.install_doc, f) 
-                 for dp, dn, filenames in os.walk(directory)  # @UnusedVariable
-                 for f in glob.glob(os.path.join(dp, '*.epub')) )
-        
-        return files
-        

distutils.ext/obidistutils/command/littlebigman.py

@@ -1,59 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os
-
-from obidistutils.command.build_exe import build_exe
-from distutils import log
-
-import subprocess
-
-class littlebigman(build_exe):
-    
-    description = "build the littlebigman executable testing endianness of the CPU"
-
-
-    def initialize_options(self):
-        build_exe.initialize_options(self)
-
-        self.littlebigman = None
-
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-        
-        build_exe.finalize_options(self)
-        
-        self.set_undefined_options('build',
-                                   ('build_temp', 'build_cexe'))
-
-        # self.ctools = self.distribution.ctools
-        
-        if os.path.isfile("distutils.ext/src/littlebigman.c"):
-            self.executables = [('littlebigman',{"sources":["distutils.ext/src/littlebigman.c"]})]
-            self.check_executable_list(self.executables)
-        else:
-            self.executables = []
-
-
-    def run_littlebigman(self):
-        p = subprocess.Popen("'%s'" % os.path.join(self.build_temp,
-                                                   'littlebigman'), 
-                             shell=True, 
-                             stdout=subprocess.PIPE)
-        little = p.communicate()[0]
-        return little.decode('latin1')
-
-    def run(self):
-        build_exe.run(self)
-        self.littlebigman=self.run_littlebigman()
-        log.info("Your CPU is in mode : %s" % self.littlebigman)
-        
-        

distutils.ext/obidistutils/command/pidname.py

@@ -1,55 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os
-
-from obidistutils.command.build_exe import build_exe
-from obidistutils.serenity.checksystem import is_mac_system
-
-
-class pidname(build_exe):
-    
-    description = "build the pidname executable returning the executable path from a PID on a mac"
-
-
-    def initialize_options(self):
-        build_exe.initialize_options(self)
-
-        self.pidname = False
-
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-        
-        build_exe.finalize_options(self)
-        
-        self.set_undefined_options('build',
-                                   ('build_scripts', 'build_cexe'))
-
-        # self.ctools = self.distribution.ctools
-        
-        if os.path.isfile("distutils.ext/src/pidname.c"):
-            self.executables = [('pidname',{"sources":["distutils.ext/src/pidname.c"]})]
-            self.check_executable_list(self.executables)
-        else:
-            self.executables = []
-
-#         self.build_cexe = os.path.join(os.path.dirname(self.build_cexe),'cbinaries') 
-#         self.mkpath(self.build_cexe)
-
-
-
-    def run(self):
-        if is_mac_system():
-            build_exe.run(self)
-            self.pidname=True
-        else:
-            self.pidname=False
-        

distutils.ext/obidistutils/command/sdist.py

@@ -1,42 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-
-import os.path
-
-from distutils.command.sdist import sdist as orig_sdist
-from distutils import dir_util
-
-class sdist(orig_sdist):
-
-    def make_distribution(self):
-        """Create the source distribution(s).  First, we create the release
-        tree with 'make_release_tree()'; then, we create all required
-        archive files (according to 'self.formats') from the release tree.
-        Finally, we clean up by blowing away the release tree (unless
-        'self.keep_temp' is true).  The list of archive files created is
-        stored so it can be retrieved later by 'get_archive_files()'.
-        """
-        # Don't warn about missing meta-data here -- should be (and is!)
-        # done elsewhere.
-        base_dir = self.distribution.get_fullname()
-        base_name = os.path.join(self.dist_dir,base_dir)
-
-        self.make_release_tree(os.path.join('tmp',base_dir), self.filelist.files)
-        archive_files = []              # remember names of files we create
-        # tar archive must be created last to avoid overwrite and remove
-        if 'tar' in self.formats:
-            self.formats.append(self.formats.pop(self.formats.index('tar')))
-
-        for fmt in self.formats:
-            file = self.make_archive(base_name, fmt, root_dir='tmp',base_dir=base_dir,
-                                     owner=self.owner, group=self.group)
-            archive_files.append(file)
-            self.distribution.dist_files.append(('sdist', '', file))
-
-        self.archive_files = archive_files
-
-        if not self.keep_temp:
-            dir_util.remove_tree(os.path.join('tmp',base_dir), dry_run=self.dry_run)

distutils.ext/obidistutils/core.py

@@ -1,226 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-from os import path
-import os.path
-import glob
-import sys
-
-# try:
-#     from setuptools.extension import Extension
-# except ImportError:
-#     from distutils.extension import Extension
-
-from distutils.extension import Extension
-
-from obidistutils.serenity.checkpackage import  install_requirements,\
-                                                check_requirements, \
-                                                RequirementError
-                                                
-from obidistutils.serenity.rerun import enforce_good_python
-from obidistutils.serenity.rerun import rerun_with_anothe_python
-from distutils import log
-
-from obidistutils.dist import Distribution
-from obidistutils.serenity import is_serenity
- 
- 
-def findPackage(root,base=None):
-    modules=[]
-    if base is None:
-        base=[]
-    for module in (path.basename(path.dirname(x)) 
-                   for x in glob.glob(path.join(root,'*','__init__.py'))):
-        modules.append('.'.join(base+[module]))
-        modules.extend(findPackage(path.join(root,module),base+[module]))
-    return modules
-    
-def findCython(root,base=None,pyrexs=None):
-    setupdir = os.path.dirname(sys.argv[0])
-    pyrexs=[]
-
-    if base is None:
-        base=[]
-    for module in (path.basename(path.dirname(x)) 
-                   for x in glob.glob(path.join(root,'*','__init__.py'))):
-                       
-                
-        for pyrex in glob.glob(path.join(root,module,'*.pyx')):
-            pyrexs.append(Extension('.'.join(base+[module,path.splitext(path.basename(pyrex))[0]]),
-                                    [pyrex]
-                                    )
-                          )
-            try:
-                cfiles = os.path.splitext(pyrex)[0]+".cfiles"
-                cfilesdir = os.path.dirname(cfiles)
-                cfiles = open(cfiles)
-                cfiles = [os.path.relpath(os.path.join(cfilesdir,y),setupdir).strip() 
-                          if y[0] !='@' else y.strip()
-                          for y in cfiles]
-                
-                log.info("Cython module : %s",cfiles)   
-                incdir = set(os.path.dirname(x) for x in cfiles if x[-2:]==".h")
-                cfiles = [x for x in cfiles if x[-2:]==".c"]                
-                pyrexs[-1].sources.extend(cfiles)
-                pyrexs[-1].include_dirs.extend(incdir)
-                pyrexs[-1].extra_compile_args.extend(['-msse2',
-                                                      '-Wno-unused-function',
-                                                      '-Wmissing-braces',
-                                                      '-Wchar-subscripts'])
-                
-            except IOError:
-                pass
-            
-        pyrexs.extend(findCython(path.join(root,module),base+[module]))
-    return pyrexs
-    
-
-def rootname(x):
-    return os.path.splitext(x.sources[0])[0]
-
-
-def prepare_commands():
-    from obidistutils.command.build import build
-    from obidistutils.command.littlebigman import littlebigman
-#    from obidistutils.command.serenity import serenity
-    from obidistutils.command.build_cexe import build_cexe
-    from obidistutils.command.build_ext import build_ext
-    from obidistutils.command.build_ctools import build_ctools
-    from obidistutils.command.build_files import build_files
-    from obidistutils.command.build_scripts import build_scripts
-    from obidistutils.command.install_scripts import install_scripts
-    from obidistutils.command.install_sphinx import install_sphinx
-    from obidistutils.command.install import install
-    from obidistutils.command.pidname import pidname
-    from obidistutils.command.sdist import sdist
-    
-        
-    
-    COMMANDS = {'build':build,
-#                'serenity':serenity,
-                'littlebigman':littlebigman,
-                'pidname':pidname,
-                'build_ctools':build_ctools, 
-                'build_files':build_files,
-                'build_cexe':build_cexe, 
-                'build_ext': build_ext,
-                'build_scripts':build_scripts, 
-                'install_scripts':install_scripts,
-                'install_sphinx':install_sphinx,
-                'install':install,
-                'sdist':sdist}
-    
-#     try:
-#         from setuptools.commands import egg_info
-#         COMMANDS['egg_info']=egg_info
-#     except ImportError:
-#         pass
-    try:
-        from obidistutils.command.build_sphinx import build_sphinx
-        COMMANDS['build_sphinx']=build_sphinx
-    except ImportError:
-        pass
-
-    return COMMANDS
-
-
-CTOOLS =[]
-CEXES  =[]
-FILES  =[]
-
-def setup(**attrs):
-    
-    log.set_threshold(log.INFO)
-    
-    minversion      = attrs.get("pythonmin",'3.4')
-    maxversion      = attrs.get('pythonmax',None)    
-    fork            = attrs.get('fork',False)
-    requirementfile = attrs.get('requirements','requirements.txt')
-
-    try:
-        del attrs['pythonmin']
-    except KeyError:
-        pass
-
-    try:
-        del attrs['pythonmax']
-    except KeyError:
-        pass
-
-    try:
-        del attrs['fork']
-    except KeyError:
-        pass
-
-    try:
-        del attrs['requirements']
-    except KeyError:
-        pass
-    
-    if is_serenity():
-    
-        
-        enforce_good_python(minversion, maxversion, fork)
-        
-        if (install_requirements(requirementfile)):
-            rerun_with_anothe_python(sys.executable,minversion,maxversion,fork)
-        
-    
-        try:
-            check_requirements(requirementfile)
-        except RequirementError as e :
-            log.error(e)                                   
-            sys.exit(1)
-        
-    if 'distclass' not in attrs:
-        attrs['distclass']=Distribution
-
-    if 'python_src' not in attrs:
-        SRC = 'python'
-    else:
-        SRC = attrs['python_src']
-        del(attrs['python_src'])
-    
-    if 'scripts' not in attrs:
-        attrs['scripts'] = glob.glob('%s/*.py' % SRC)
-
-    if 'package_dir' not in attrs:
-        attrs['package_dir'] = {'': SRC}
-
-    if 'packages' not in attrs:
-        attrs['packages'] = findPackage(SRC)
-    
-    if 'cmdclass' not in attrs:
-        attrs['cmdclass'] = prepare_commands()
-
-    if 'ctools' not in attrs:
-        attrs['ctools'] = CTOOLS
-    
-    if 'executables' not in attrs:
-        attrs['executables'] = CEXES
-        
-    if 'files' not in attrs:
-        attrs['files'] = FILES
-        
-    if 'sse' not in attrs:
-        attrs['sse']=None
-        
-    if 'serenity' not in attrs:
-        attrs['serenity']=False
-    
-    EXTENTION=findCython(SRC)
-    
-    if 'ext_modules' not in attrs:
-        attrs['ext_modules'] = EXTENTION
-        
-#     try:
-#         from setuptools.core import setup as ori_setup
-#     except ImportError:
-#         from distutils.core import setup as ori_setup
-
-    from distutils.core import setup as ori_setup
-    
-    ori_setup(**attrs)

distutils.ext/obidistutils/dist.py

@@ -1,58 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-# try:
-#     from setuptools.dist import Distribution as ori_Distribution
-# except ImportError:
-#     from distutils.dist import Distribution as ori_Distribution
-
-from distutils.dist import Distribution as ori_Distribution
-
-class Distribution(ori_Distribution):
-    
-    def __init__(self,attrs=None):
-        self.executables = None
-        self.ctools = None
-        self.files = None
-        self.build_cexe  = None
-        self.deprecated_scripts = None
-        self.zip_safe=False
-        self.sse = None
-        self.serenity=attrs['serenity']
-        
-        ori_Distribution.__init__(self, attrs)
-        
-        self.global_options.insert(0,('serenity', None, "install or build the package in a python virtualenv "
-                                                       "without polluting the installed python and with many "
-                                                       "checks during the installation process"
-                                     ))
-        self.global_options.insert(0,('virtualenv', None, "if the installation is done using the serenity mode "
-                                                        "this option allows for specifying the virtualenv name. "
-                                                        "By default the name is PACKAGE-VERSION"
-                                     ))
-        
-    def run_commands(self):
-        """Run each command that was seen on the setup script command line.
-        Uses the list of commands found and cache of command objects
-        created by 'get_command_obj()'.
-        """
-#        self.run_command('littlebigman')
-        ori_Distribution.run_commands(self)
-        
-        
-    def has_executables(self):
-        return self.executables is not None and self.executables
-        
-    def has_ctools(self):
-        return self.ctools is not None and self.ctools
-        
-    def has_files(self):
-        return self.files is not None and self.files
-        
-    def has_deprecated_scripts(self):
-        return self.deprecated_scripts is not None and self.deprecated_scripts
-
-    

distutils.ext/obidistutils/serenity/__init__.py

@@ -1,112 +0,0 @@
-import sys
-
-from distutils import util
-from distutils import sysconfig
-from distutils import log
-from distutils.version import LooseVersion, StrictVersion
-import glob
-import os
-import subprocess
-import re 
-from distutils.errors import DistutilsError
-import tempfile
-
-from importlib.util import spec_from_file_location  # @UnresolvedImport
-import zipimport
-
-import argparse
-
-import base64
-
-from .checkpython import is_python_version
-                        
-                        
-from obidistutils.serenity.rerun import  enforce_good_python
-from obidistutils.serenity.rerun import rerun_with_anothe_python
-
-from obidistutils.serenity.virtual import serenity_virtualenv
-                        
-from obidistutils.serenity.checksystem import is_mac_system, \
-                                              is_windows_system
-                        
-from obidistutils.serenity.checkpackage import install_requirements
-from obidistutils.serenity.checkpackage import check_requirements
-
-from obidistutils.serenity.util import save_argv
-                        
-from obidistutils.serenity.snake import snake
-                            
-    
-def serenity_snake(envname,package,version):
-    old = log.set_threshold(log.INFO)
-
-    log.info("Installing %s (%s) in serenity mode" % (package,version))
-
-    enforce_good_python()
-
-    virtualpython=serenity_virtualenv(envname,package,version)
-    
-    if virtualpython!=os.path.realpath(sys.executable):
-        log.info("Restarting installation within the %s virtualenv" % (envname))
-        rerun_with_anothe_python(virtualpython)
-        
-    log.info("%s will be installed with python : %s" % (package,virtualpython))
-        
-    if install_requirements():    
-        log.info("Restarting installation with all dependencies ok")
-        rerun_with_anothe_python(virtualpython)
-    
-    log.set_threshold(old)
-    
-def serenity_assert(version):
-    check_requirements()
-
-
-def is_serenity():
-    from obidistutils.serenity.globals import local_serenity
-    return local_serenity and local_serenity[0]
-
-def serenity_mode(package,version):
-    
-    save_argv()
-
-    
-    from obidistutils.serenity.globals import saved_args
-    from obidistutils.serenity.globals import local_serenity
-    
-
-    old = log.set_threshold(log.INFO)
-    
-    argparser = argparse.ArgumentParser(add_help=False)
-    argparser.add_argument('--serenity',
-                           dest='serenity', 
-                           action='store_true',
-                           default=False, 
-                           help='Switch the installer in serenity mode. Everythings are installed in a virtualenv')
-
-    argparser.add_argument('--virtualenv',
-                           dest='virtual', 
-                           type=str,
-                           action='store',
-                           default="%s-%s" % (package,version), 
-                           help='Specify the name of the virtualenv used by the serenity mode [default: %s-%s]' % (package,version))    
-    
-    args, unknown = argparser.parse_known_args()
-    sys.argv = [sys.argv[0]] + unknown
-    
-    if args.serenity:
-        local_serenity.append(True)
-        serenity_snake(args.virtual,package,version)
-    else:
-        local_serenity.append(False)       
-    
-    log.set_threshold(old)
-    
-    return args.serenity
-    
-    
-def getVersion(source,main,version):
-    path  = os.path.join(source,main,'%s.py' % version)
-    spec = spec_from_file_location('version',path)
-    return spec.loader.load_module().version.strip()
-    

distutils.ext/obidistutils/serenity/checkpackage.py

@@ -1,160 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-import re
-import os
-
-import pip                                              # @UnresolvedImport
-from pip.utils import get_installed_distributions       # @UnresolvedImport
-from distutils.version import StrictVersion             # @UnusedImport
-from distutils.errors import DistutilsError
-from distutils import log
-
-class RequirementError(Exception):
-    pass
-
-def is_installed(requirement):
-    
-    
-    requirement_project,requirement_relation,requirement_version = parse_package_requirement(requirement)
-    
-    package = [x for x in get_installed_distributions() if x.project_name==requirement_project]
-    
-    if len(package)==1:
-        if requirement_version is not None and requirement_relation is not None:    
-            rep = (len(package)==1) and eval("StrictVersion('%s') %s StrictVersion('%s')" % (package[0].version,
-                                                                                           requirement_relation,
-                                                                                           requirement_version)
-                                             )
-        else:
-            rep=True
-    else:
-        rep=False
-    
-    if rep:
-        if requirement_version is not None and requirement_relation is not None:        
-            log.info("Look for package %s (%s%s) : ok version %s installed" % (requirement_project,
-                                                                               requirement_relation,
-                                                                               requirement_version,
-                                                                               package[0].version))
-        else:
-            log.info("Look for package %s : ok version %s installed" % (requirement_project,
-                                                                        package[0].version))
-    else:
-        if len(package)!=1:
-            log.info("Look for package %s (%s%s) : not installed" % (requirement_project,
-                                                                     requirement_relation,
-                                                                     requirement_version))
-        else:
-            log.info("Look for package %s (%s%s) : failed only version %s installed" % (requirement_project,
-                                                                                        requirement_relation,
-                                                                                        requirement_version,
-                                                                                        package[0].version))
-        
-    return rep
-
-
-def get_requirements(requirementfile='requirements.txt'):
-    
-    try:
-        requirements = open(requirementfile).readlines()
-        requirements = [x.strip() for x in requirements]
-        requirements = [x for x in requirements if x[0]!='-']
-    
-    except IOError:
-        requirements = []
-        
-    return requirements
-    
-    
-def install_requirements(requirementfile='requirements.txt'):
-    
-    install_something=False
-
-    requirements = get_requirements(requirementfile)
-
-    log.info("Required packages for the installation :")
-    for x in requirements:
-        ok = is_installed(x)
-        if not ok:
-            log.info("  Installing requirement : %s" % x)
-            pip_install_package(x)
-            install_something=True
-            if x[0:3]=='pip':
-                return True
-                
-    return install_something
- 
-
-def check_requirements(requirementfile='requirements.txt'):
-    
-    requirements = get_requirements(requirementfile)
-    
-    log.info("Required packages for the installation :")
-    for x in requirements:
-        ok = is_installed(x)
-        if not ok:
-            raise RequirementError("  Missing requirement : %s -- Package installation stopped" % x)
-                
- 
-
-
-def parse_package_requirement(requirement):
-    
-    version_pattern = re.compile('[=><]+(.*)$')
-    project_pattern  = re.compile('[^=><]+')
-    relationship_pattern = re.compile('[=><]+')
-    
-    try:
-        requirement_project = project_pattern.search(requirement).group(0)
-        requirement_version = version_pattern.search(requirement)
-        if requirement_version is not None:
-            requirement_version=requirement_version.group(1)
-        requirement_relation= relationship_pattern.search(requirement)
-        if requirement_relation is not None:
-            requirement_relation=requirement_relation.group(0)
-    except:
-        raise DistutilsError("Requirement : %s not correctly formated" % requirement)
-    
-    return requirement_project,requirement_relation,requirement_version
-    
-
-def get_package_requirement(package,requirementfile='requirements.txt'):            
-    requirements = get_requirements(requirementfile)
-    req = [x for x in requirements
-             if x[0:len(package)]==package
-          ]
-    
-    if len(req)==1:
-        return req[0]
-    else:
-        return None
-        
-        
-def pip_install_package(package,directory=None,upgrade=True):
-
-    if directory is not None:
-        log.info('    installing %s in directory %s' % (package,str(directory)))
-        
-
-    if 'http_proxy' in os.environ and 'https_proxy' not in os.environ:
-        os.environ['https_proxy']=os.environ['http_proxy']
-
-    args = ['install']
-    
-    if upgrade:
-        args.append('--upgrade')
-    
-    if 'https_proxy' in os.environ:
-        args.append('--proxy=%s' % os.environ['https_proxy'])
-        
-    if directory is not None:
-        args.append('--target=%s' % directory)
-    
-    args.append(package)
-        
-    return pip.main(args)
-

distutils.ext/obidistutils/serenity/checkpython.py

@@ -1,138 +0,0 @@
-'''
-Created on 24 mai 2015
-
-@author: coissac
-'''
-from distutils.version import StrictVersion
-from distutils import sysconfig
-import subprocess
-import os
-import glob
-import re
-
-from obidistutils.serenity.checksystem import is_windows_system
-import sys
-
-
-def is_python_version(path=None,minversion='3.4',maxversion=None):
-    '''
-    Checks that the python version is in the range {minversion,maxversion[
-    
-        @param path: if None consider the running python
-                     otherwise the python pointed by the path
-        @param minversion: the minimum version to consider
-        @param maxversion: the maximum version to consider (strictly inferior to)
-                     
-        @return: True if the python version match
-        @rtype: bool
-    '''
-    if path is None:
-        pythonversion = StrictVersion(sysconfig.get_python_version())
-    else:
-        command = """'%s' -c 'from distutils import sysconfig; """ \
-                  """print(sysconfig.get_python_version())'""" % path
-                  
-        p = subprocess.Popen(command, 
-                             shell=True, 
-                             stdout=subprocess.PIPE)
-        pythonversion=str(p.communicate()[0],'utf8').strip()
-        pythonversion = StrictVersion(pythonversion)
-                        
-    return  (        pythonversion >=StrictVersion(minversion) 
-             and (   maxversion is None    
-                  or pythonversion < StrictVersion(maxversion))
-            )
-           
-
-def lookfor_good_python(minversion='3.4',maxversion=None,followLink=False):
-    '''
-    Look for all python interpreters present in the system path that
-    match the version constraints.
-    
-    @param minversion: the minimum version to consider
-    @param maxversion: the maximum version to consider (strictly inferior to)
-    @param followLink: a boolean value indicating if link must be substituted 
-                       by their real path.
-                       
-    @return: a list of path to interpreters
-    '''
-    exe = []
-    if not is_windows_system():
-        paths = os.environ['PATH'].split(os.pathsep)
-        for p in paths:
-            candidates = glob.glob(os.path.join(p,'python*')) 
-            pexe = []
-            pythonpat=re.compile('python([0-9]|[0-9]\.[0-9])?$')
-            for e in candidates:
-                print(e)
-                if pythonpat.search(e) is not None:
-                    if followLink and os.path.islink(e):
-                        e = os.path.realpath(e)
-                    if (os.path.isfile(e) and 
-                       os.access(e, os.X_OK) and 
-                       is_python_version(e,minversion,maxversion)):
-                        pexe.append(e)
-            exe.extend(set(pexe))
-        
-    return exe
-
-def is_a_virtualenv_python(path=None):
-    '''
-    Check if the python is belonging a virtualenv
-    
-        @param path: the path pointing to the python executable.
-                     if path is None then the running python is
-                     considered.
-        @param path: str or None 
-                     
-        @return: True if the python belongs a virtualenv
-                 False otherwise
-        @rtype: bool
-                 
-    '''
-    if path is None:
-        rep = sys.base_exec_prefix != sys.exec_prefix
-    else:
-        command = """'%s' -c 'import sys; print(sys.base_exec_prefix != sys.exec_prefix)'""" % path
-        p = subprocess.Popen(command, 
-                             shell=True, 
-                             stdout=subprocess.PIPE)
-        rep = eval(str(p.communicate()[0],'utf8'))
-        
-    return rep
-
-
-def which_virtualenv(path=None,full=False):
-    '''
-    Returns the name of the virtualenv.
-        @param path: the path to a python binary or None
-                     if you want to consider the running python
-        @type path: str or None
-                     
-        @param full: if set to True, returns the absolute path,
-                     otherwise only return a simple directory name
-        @type full: bool
-                 
-        @return: the virtual environment name or None if the
-                 path does not belong a virtualenv
-        @rtype: str or None
-    '''
-    if path is None:
-        path = sys.executable
-    
-    if is_a_virtualenv_python(path):
-        parts = path.split(os.sep)
-        try:
-            if full:
-                rep = os.sep.join(parts[0:parts.index('bin')])
-                rep = os.path.realpath(rep)
-            else:
-                rep = parts[parts.index('bin')-1]
-        except ValueError:
-            rep = None
-    else:
-        rep=None
-        
-    return rep
-        
-

distutils.ext/obidistutils/serenity/checksystem.py

@@ -1,18 +0,0 @@
-'''
-Created on 24 mai 2015
-
-@author: coissac
-'''
-
-from distutils import util
-
-def is_mac_system():
-    platform = util.get_platform().split('-')[0]
-    
-    return platform=='macosx'
-
-def is_windows_system():
-    platform = util.get_platform().split('-')[0]
-    
-    return platform=='Windows'
-        

distutils.ext/obidistutils/serenity/globals.py

@@ -1,14 +0,0 @@
-'''
-Created on 24 mai 2015
-
-@author: coissac
-'''
-
-
-saved_args=[]
-tmpdir=[]
-local_pip=[]
-local_virtualenv=[]
-local_cython=[]
-local_serenity=[]
-        

distutils.ext/obidistutils/serenity/rerun.py

@@ -1,61 +0,0 @@
-'''
-Created on 24 mai 2015
-
-@author: coissac
-'''
-
-import sys
-import os
-from distutils import log
-from distutils.errors import DistutilsError
-
-
-from obidistutils.serenity.globals import saved_args
-from obidistutils.serenity.checkpython import is_python_version,\
-    lookfor_good_python
-
-
-def rerun_with_anothe_python(path, minversion='3.4',maxversion=None, fork=False):
-        
-    if saved_args:
-        args = saved_args
-    else:
-        args = list(sys.argv)
-        
-          
-    assert is_python_version(path,minversion,maxversion), \
-           'the selected python is not adapted to the installation of this package'
-                   
-    args.insert(0, path)
-        
-    sys.stderr.flush()
-    sys.stdout.flush()
-    
-    if fork:
-        log.info('Forking a new install process')
-        os.system(' '.join(list(args)))
-        log.info('External process ended')
-        sys.exit(0)
-    else:
-        log.info('Install script restarting...')
-        os.execv(path,list(args))
-
-def enforce_good_python(minversion='3.4',maxversion=None, fork=False):
-    if is_python_version(minversion=minversion,maxversion=maxversion):
-        log.info('You are running the good python')
-        return True
-    
-    goodpython = lookfor_good_python(minversion,maxversion)
-    
-    if not goodpython:
-        raise DistutilsError('No good python identified on your system')
-
-    goodpython=goodpython[0]
-    
-    log.warn("========================================")    
-    log.warn("")
-    log.warn("    Switching to python : %s" % goodpython)
-    log.warn("")
-    log.warn("========================================")    
-
-    rerun_with_anothe_python(goodpython)

distutils.ext/obidistutils/serenity/snake.py

@@ -1,35 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-snake ="""
-
-        ___
-      ,'._,`.
-     (-.___.-)
-     (-.___.-)
-     `-.___.-'
-      ((  @ @|              .            __
-       \   ` |         ,\   |`.    @|   |  |      _.-._
-      __`.`=-=mm===mm:: |   | |`.   |   |  |    ,'=` '=`.
-     (    `-'|:/  /:/  `/  @| | |   |, @| @|   /---)W(---\ 
-      \ \   / /  / /         @| |   '         (----| |----) ,~
-      |\ \ / /| / /            @|              \---| |---/  |
-      | \ V /||/ /                              `.-| |-,'   |
-      |  `-' |V /                                 \| |/    @'
-      |    , |-'                                 __| |__
-      |    .;: _,-.                         ,--""..| |..""--.
-      ;;:::' "    )                        (`--::__|_|__::--')
-    ,-"      _,  /                          \`--...___...--'/
-   (    -:--'/  /                           /`--...___...--'\  
-    "-._  `"'._/                           /`---...___...---'\  
-        "-._   "---.                      (`---....___....---')
-         .' ",._ ,' )                     |`---....___....---'|
-         /`._|  `|  |                     (`---....___....---')
-        (   \    |  /                      \`---...___...---'/
-         `.  `,  ^""                        `:--...___...--;'
-           `.,'               hh              `-._______.-'
-
-"""

distutils.ext/obidistutils/serenity/util.py

@@ -1,27 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-import sys 
-import tempfile
-
-
-from obidistutils.serenity.globals import tmpdir         # @UnusedImport
-from obidistutils.serenity.globals import saved_args     # @UnusedImport
-
-def get_serenity_dir():
-    global tmpdir
-
-    if not tmpdir:
-        tmpdir.append(tempfile.mkdtemp())
-    return tmpdir[0]
-        
-def save_argv():
-    global saved_args
-
-    del saved_args[:]
-    saved_args.extend(list(sys.argv))
-
-           

distutils.ext/obidistutils/serenity/virtual.py

@@ -1,69 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-import os
-import sys
-import venv
-
-from distutils.errors import DistutilsError
-from .globals import local_virtualenv  # @UnusedImport
-from .checkpython import   which_virtualenv,\
-                           is_python_version, \
-                           is_a_virtualenv_python
-                                                
-
-    
-    
-def serenity_virtualenv(envname,package,version,minversion='3.4',maxversion=None):
-        
-    #
-    # Checks if we are already running under the good virtualenv
-    #
-    ve = which_virtualenv(full=True)
-    if ve == os.path.realpath(envname) and is_python_version(minversion=minversion,maxversion=maxversion):
-        return sys.executable
-        
-    #
-    # Check if the virtualenv exist
-    # 
-        
-    python = None
-    
-    if os.path.isdir(envname):
-        python = os.path.join(envname,'bin','python')
-        ok = (is_python_version(python,
-                                minversion=minversion,
-                                maxversion=maxversion) and 
-              is_a_virtualenv_python(python))
-        
-        
-        #
-        # The virtualenv already exist but it is not ok
-        #
-        if not ok:
-            raise DistutilsError("A virtualenv %s already exists but not with the required python")
-                 
-    else:
-        ok = False
-                
-        
-    #
-    # Creates a new virtualenv
-    #
-    if not ok:
-        venv.create(envname, 
-                    system_site_packages=False, 
-                    clear=True, 
-                    symlinks=False, 
-                    with_pip=True)
-        
-        # check the newly created virtualenv
-        return serenity_virtualenv(envname,package,version)
-    
-    return os.path.realpath(python)
-    
-    
-    

distutils.ext/src/littlebigman.c

@@ -1,24 +0,0 @@
-/*
- * littlebigman.c
- *
- *  Created on: 11 juil. 2012
- *      Author: coissac
- */
-
-#include<stdio.h>
-
-int main(int argc, char *argv[])
-{
-    union { int entier;
-            char caractere[4] ;
-    } test;
-
-    test.entier=0x01020304;
-
-    if (test.caractere[3] == 1)
-       printf("-DLITTLE_END");
-    else
-        printf("-DBIG_END");
-
-	return 0;
-}

distutils.ext/src/pidname.c

@@ -1,24 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <errno.h>
-#include <libproc.h>
-
-int main (int argc, char* argv[])
-{
-	pid_t pid; int ret;
-	char pathbuf[PROC_PIDPATHINFO_MAXSIZE];
-
-	if ( argc > 1 ) {
-		pid = (pid_t) atoi(argv[1]);
-		ret = proc_pidpath (pid, pathbuf, sizeof(pathbuf));
-		if ( ret <= 0 ) {
-			fprintf(stderr, "PID %d: proc_pidpath ();\n", pid);
-			fprintf(stderr,	"    %s\n", strerror(errno));
-		} else {
-			printf("proc %d: %s\n", pid, pathbuf);
-		}
-	}
-
-	return 0;
-}

doc/.gitignore

@@ -1,3 +0,0 @@
-/build/
-/doxygen/
-/build_dir.txt

doc/Makefile

@@ -1,203 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = build
-DOXYGENDIR    = doxygen
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
-
-help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  dirhtml    to make HTML files named index.html in directories"
-	@echo "  singlehtml to make a single large HTML file"
-	@echo "  pickle     to make pickle files"
-	@echo "  json       to make JSON files"
-	@echo "  htmlhelp   to make HTML files and a HTML help project"
-	@echo "  qthelp     to make HTML files and a qthelp project"
-	@echo "  applehelp  to make an Apple Help Book"
-	@echo "  devhelp    to make HTML files and a Devhelp project"
-	@echo "  epub       to make an epub"
-	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
-	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
-	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
-	@echo "  text       to make text files"
-	@echo "  man        to make manual pages"
-	@echo "  texinfo    to make Texinfo files"
-	@echo "  info       to make Texinfo files and run them through makeinfo"
-	@echo "  gettext    to make PO message catalogs"
-	@echo "  changes    to make an overview of all changed/added/deprecated items"
-	@echo "  xml        to make Docutils-native XML files"
-	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
-	@echo "  linkcheck  to check all external links for integrity"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
-	@echo "  coverage   to run coverage check of the documentation (if enabled)"
-
-clean:
-	rm -rf $(BUILDDIR)/*
-	rm -rf $(DOXYGENDIR)/*
-
-html:
-	@echo "Generating Doxygen documentation..."
-	doxygen Doxyfile
-	@echo "Doxygen documentation generated. \n"
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
-	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
-	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
-	@echo
-	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
-	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
-	@echo
-	@echo "Build finished; now you can process the pickle files."
-
-json:
-	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
-	@echo
-	@echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
-	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
-	@echo
-	@echo "Build finished; now you can run HTML Help Workshop with the" \
-	      ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
-	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
-	@echo
-	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
-	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/OBITools-3.qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/OBITools-3.qhc"
-
-applehelp:
-	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
-	@echo
-	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
-	@echo "N.B. You won't be able to view it unless you put it in" \
-	      "~/Library/Documentation/Help or install it in your application" \
-	      "bundle."
-
-devhelp:
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/OBITools-3"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/OBITools-3"
-	@echo "# devhelp"
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doc/doxygen/xml/.gitignore

@@ -1,4 +0,0 @@
-# Ignore everything in this directory
-*
-# Except this file
-!.gitignore

doc/sphinx/source/DMS.rst

@@ -1,160 +0,0 @@
-*********************************************
-The OBItools3 Data Management System (OBIDMS)
-*********************************************
-
-A complete DNA metabarcoding experiment relies on several kinds of data.
-
-	- The sequence data resulting from the sequencing of the PCR products,
-	- The description of the samples including all their metadata,
-	- One or several reference databases used for the taxonomic annotation,
-	- One or several taxonomy databases.
-
-Up to now, each of these categories of data were stored in separate
-files, and nothing made it mandatory to keep them together.
-
-
-The `Data Management System` (DMS) of OBITools3 can be regarded as a basic 
-database system.
-
-
-OBIDMS UML
-==========
-
-.. image:: ./UML/OBIDMS_UML.png
-
-:download:`html version of the OBIDMS UML file <UML/ObiDMS_UML.class.violet.html>`
-
-
-An OBIDMS directory contains :
-  * one `OBIDMS history file <#obidms-history-files>`_
-  * Two different kinds of directories :
-     * OBIDMS column directories
-     * OBIDMS column group directories containing OBIDMS column directories
-
-
-OBIDMS column directories
-=========================
-
-OBIDMS column directories contain :
-    * all the different versions of one OBIDMS column, under the form of different files (`OBIDMS column files <#obidms-column-files>`_)
-    * one `OBIDMS version file <#obidms-version-files>`_
-
-The directory name is the column attribute, or sub-attribute if the column directory is in a column group directory.
-
-
-OBIDMS column group directories
-===============================
-
-OBIDMS column group directories contain OBIDMS column directories. They are used to store dictionary-like data, where 
-each key corresponds to an OBIDMS column.
-
-The directory name is the dictionary attribute. Each key is considered a sub-attribute and is associated to its column.
-
-
-OBIDMS column files
-===================
-
-Each OBIDMS column file contains :
-	* a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes
-	  on most systems) containing metadata
-	* one column of data with the same `OBIType <types.html#obitypes>`_
-
-
-Header
-------
-
-The header of an OBIDMS column contains :
-
-	* Endian byte order
-	* Header size (PAGESIZE multiple)
-	* Number of lines of data
-	* Number of lines of data used
-	* `OBIType <types.html#obitypes>`_ (type of the data)
-	* Date of creation of the file
-	* Version of the OBIDMS column
-	* The column name
-	* Eventual comments
-
-
-Data
-----
-
-A column of data with the same `OBIType <types.html#obitypes>`_.
-
-
-Mandatory columns
------------------
-
-Some columns must exist in an OBIDMS directory :
-    * sequence identifiers column (type ``OBIStr_t``)
-
-
-File name
----------
-
-Each file is named with the attribute associated to the data it contains, and the number of
-its version, separated by an ``@``, and with the extension ``.odc``.
-
-Example : ``count@3.odc``
-
-
-Modifications
--------------
-
-An OBIDMS column file can only be modified by the process that created it, and while its status is set to Open. 
-
-When a process wants to modify an OBIDMS column file that is closed, it must first clone it. Cloning creates a new version of the
-file that belongs to the process, i.e., only that process can modify that file, as long as its status is set to Open. Once the process
-has finished writing the new version of the column file, it sets the column file's status to Closed, and the file can never be modified
-again.
-
-That means that one column is stored in one file (if there is only one version)
-or more (if there are several versions), and that there is one file per version.
-
-All the versions of one column are stored in one directory.
-
-
-Versioning
-----------
-
-The first version of a column file is numbered 0, and each new version increments that
-number by 1.
-
-The number of the latest version of an OBIDMS column is stored in the `OBIDMS version file <#obidms-version-files>`_ of its directory.
-
-
-OBIDMS version files
-====================
-
-Each OBIDMS column is associated with an OBIDMS version file in its directory, that contains the number of the latest
-version of the column.
-
-File name
----------
-
-OBIDMS version files are named with the attribute associated to the data contained in the column, and
-have the extension ``.odv``.
-
-Example : ``count.odv``
-
-
-OBIDMS views
-============
-
-An OBIDMS view consists of a list of OBIDMS columns and lines. A view includes one version
-of each mandatory column. Only one version of each column is included. All the columns of
-one view contain the same number of lines in the same order.
-
-
-OBIDMS history file
-===================
-
-An OBIDMS history file consists of an ordered list of views and commands, those commands leading
-from one view to the next one.
-
-This history can be represented in the form of a ?? showing all the
-operations ever done in the OBIDMS directory and the views in between them :
-
-.. image:: ./images/history.png
-    :width: 150 px
-    :align: center

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doc/sphinx/source/conf.py

@@ -1,298 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# OBITools3 documentation build configuration file, created by
-# sphinx-quickstart on Mon May  4 14:36:57 2015.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-import sys
-import os
-import shlex
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.pngmath',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'breathe',
-]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'OBITools3'
-copyright = u'2015, Céline Mercier, Eric Coissac, Frédéric Boyer'
-author = u'Céline Mercier, Eric Coissac, Frédéric Boyer'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '0.0'
-# The full version, including alpha/beta/rc tags.
-release = '0.0.0'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = []
-
-# The reST default role (used for this markup: `text`) to use for all
-# documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-# If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-html_theme = 'bizstyle'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#html_theme_options = {}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents.  If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-#html_logo = None
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# Add any extra paths that contain custom files (such as robots.txt or
-# .htaccess) here, relative to this directory. These files are copied
-# directly to the root of the documentation.
-#html_extra_path = []
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_domain_indices = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it.  The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Language to be used for generating the HTML full-text search index.
-# Sphinx supports the following languages:
-#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
-#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
-#html_search_language = 'en'
-
-# A dictionary with options for the search language support, empty by default.
-# Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
-
-# The name of a javascript file (relative to the configuration directory) that
-# implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'OBITools3doc'
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-  (master_doc, 'OBITools3.tex', u'OBITools3 Documentation',
-   u'Céline Mercier, Eric Coissac, Frédéric Boyer', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'obitools3', u'OBITools3 Documentation',
-     [author], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-  (master_doc, 'OBITools3', u'OBITools3 Documentation',
-   author, 'OBITools3', 'One line description of project.',
-   'Miscellaneous'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-#texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
-
-#Breathe configuration
-sys.path.append( "../breathe/" )
-breathe_projects = { "OBITools3": "../doxygen/xml/" }
-breathe_default_project = "OBITools3"
-

doc/sphinx/source/containers.rst

@@ -1,29 +0,0 @@
-===============
-Container types
-===============
-
-Containers allow to manage collections of values of homogeneous type.
-Three container types exist.
-
-A container is a non-mutable structure once it has been locked.
-Consequently, only insertion procedures are needed.
-
-Lists
------
-
-Correspond to an ordered collection of values belonging to an elementary type.
-
-At its creation, ...
-
-
-Sets
-----
-
-Correspond to an unordered collection of values belonging to an elementary type.
-
-
-Dictionaries
-------------
-
-Dictionaries allow to associate a `key` to a `value`. Values can be retrieved through their associated key.
-Values must belong to an elementary type and keys must be *OBIStr_t*.

doc/sphinx/source/data.rst

@@ -1,16 +0,0 @@
-#################
-Data in OBITools3
-#################
-
-The OBITools3 inaugure a new way to manage DNA metabarcoding data. 
-They rely on a `Data management System` (DMS) that can be considered as
-a simplified database system.
-
-
-.. toctree::
-   :maxdepth: 2
-
-   The data management system <DMS>
-   The data types <types>
-
-

doc/sphinx/source/elementary.rst

@@ -1,40 +0,0 @@
-================
-Elementary types
-================
-
-They correspond to simple values.
-
-Atomic types
-------------
-
-=========   =========   ============   ==============================
- Type        C type      OBIType        Definition
-=========   =========   ============   ==============================
- integer     int32_t     OBIInt_t       a signed integer value
- float       double      OBIFloat_t     a floating value
- boolean     bool        OBIBool_t      a boolean true/false value
- char        char        OBIChar_t      a character
- index       size_t      OBIIdx_t       an index in a data structure
-=========   =========   ============   ==============================
-
-
-The composite types
--------------------
-
-Character string type
-.....................
-
-================   ======   ========   ==================
-Type               C type   OBIType    Definition
-================   ======   ========   ==================
-Character string   ?        OBIStr_t   a character string
-================   ======   ========   ==================
-
-The taxid type
-..............
-
-====================   ======   ==========   ======================
-Type                   C type   OBIType      Definition
-====================   ======   ==========   ======================
-Taxonomic identifier   size_t   OBITaxid_t   a taxonomic identifier
-====================   ======   ==========   ======================

doc/sphinx/source/guidelines.rst

@@ -1,132 +0,0 @@
-######################
-Programming guidelines
-######################
-
-
-***************
-Version control
-***************
-
-Version control is managed with `Git <http://git-scm.com/>`_. 
-Issue tracking and repository management are done using `GitLab <https://about.gitlab.com/>`_ 
-at http://git.metabarcoding.org/.
-
-
-Branching strategy
-==================
-
-
-Master branch
--------------
-
-The master branch should only contain functional scripts. 
-
-
-Topic branches
---------------
-
-Topic branches should correspond to development branches revolving around a topic corresponding 
-to the branch's name.
-
-
-Release branches
-----------------
-
-Release branches should start with duplicates of tags and be used to patch them. 
-
-
-Tags
-----
-
-Tags should never be committed to.
-
-
-Rebasing
---------
-
-Rebasing should be avoided on the distant server.
-
-
-Merging
--------
-
-Merging should never overwrite on a release branch or on a tag.
-
-
-Branching strategy diagram
---------------------------
-
-.. image:: ./images/version_control.png
-
-
-Issue tracking
-==============
-
-Issue tracking is done using `GitLab <https://about.gitlab.com/>`_ at http://git.metabarcoding.org/.
-Tickets should always be labeled with the branches for which they are relevant.
-
-
-*************
-Documentation
-*************
-
-C functions are documented in the header files.
-
-
-**************
-OBITools3 wiki
-**************
-
-The OBITools3 wiki is managed with GitLab.
-
-
-*********************
-Programming languages
-*********************
-
-C99 :
-	* All the low-level input/output functions (e.g. all the `OBIDMS <formats.html#the-obitools3-data-management-system-obidms>`_ functions)
-	* Computing-intensive code (e.g. alignment or pattern matching)
-	
-`Cython <cython.org>`_ :
-	* Object layer
-	* OBITools3 library
-
-`Python 3 <https://www.python.org/>`_ :
-	* Top layer code (scripts)	
-	
-For the documentation, `Sphinx <http://sphinx-doc.org/>`_ should be used for both the original 
-documentation and for the generation of documentation from the python code. `Doxygen <http://www.stack.nl/~dimitri/doxygen/>`_ 
-should be used for the generation of documentation from the C code, which should be then integrated 
-in the Sphinx documentation using `Breathe <https://breathe.readthedocs.org/en/latest/>`_.
-
-
-******************
-Naming conventions
-******************
-
-Struct, Enum:                                   ``Title_case``
-
-Enum members, macros, constants:                ``ALL_CAPS``
-
-Functions, local variables:                     ``lower_case``
-
-Functions that shouldn't be called directly:    ``_lower_case`` (``_`` prefix)
-
-Global variables:                                ``g_lower_case`` (``g_`` prefix)
-
-Pointers:                                        ``pointer_ptr`` (``_ptr`` suffix)
-
-.. note::
-    Underscores are used to delimit 'words'.
-
-.. todo::
-    ``obi_function`` for public functions names?
-
-
-*****************
-Programming rules
-*****************
-
-    * 
-

doc/sphinx/source/index.rst

@@ -1,22 +0,0 @@
-.. OBITools3 documentation master file, created by
-   sphinx-quickstart on Mon May  4 14:36:57 2015.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-OBITools3 documentation
-==========================
-
-.. toctree::
-   :maxdepth: 2
-
-   Programming guidelines <guidelines>
-   Data structures <data>
-   Pistes de reflexion <pistes>
-
-
-Indices and tables
-------------------
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

doc/sphinx/source/pistes.rst

@@ -1,23 +0,0 @@
-###################
-Pistes de reflexion
-###################
-
-
-******************************
-Ce que l'on veut pouvoir faire
-******************************
-
-    * Gerer les valeurs manquantes
-    * Modifier une colonne en cours d'ecriture (mmap)
-    * Ajouter des valeurs a la fin du fichier d'une colonne en cours d'ecriture (mmap)
-    
-
-******
-Divers
-******
-
-* Si l'ordre d'une colonne est change, elle est reecrite (pas d'index).
-* Utilisation de semaphores pour la lecture
-* Utilisation de tas pour l'indexation des chaines de caracteres. Chaque colonne dont 
-  le type est OBIStr_t est stockee dans 3 fichiers : un fichier contenant les chaines, un 
-  fichier contenant les index, et un fichier contenant le tas.

doc/sphinx/source/specialvalues.rst

@@ -1,52 +0,0 @@
-==============
-Special values
-==============
-
-
-NA values
-=========
-
-All OBITypes have an associated NA (Not Available) value. 
-NA values are implemented by specifying an explicit NA value for each type, corresponding to the R standards:
-
-* For the types ``OBIInt_t``, ``OBIBool_t``, ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``INT_MIN``.
-
-* For the type ``OBIChar_t``: the NA value is ``\0`` (?).
-
-* For the type ``OBIStr_t`` : the NA value is ``\0`` (?).
-
-* For the type ``OBIFloat_t``::
-
-    typedef union
-    {
-        double value;
-        unsigned int word[2];
-    } ieee_double;
-    
-    static double NA_value(void)
-    {
-        volatile ieee_double x;
-        x.word[hw] = 0x7ff00000;
-        x.word[lw] = 1954;
-        return x.value;
-    }   
-
-
-Minimum and maximum values for ``OBIInt_t``
-===========================================
-
-* Maximum value : ``INT_MAX``
-* Minimum value : ``INT_MIN(-1?)``
-
-
-Infinity values for the type ``OBIFloat_t``
-===========================================
-
-* Positive infinity : ``INFINITY`` (should be defined in ``<math.h>``)
-* Negative infinity : ``-INFINITY``
-
-
-NaN value for the type ``OBIFloat_t``
-=====================================
-
-* NaN (Not a Number) value : ``NAN`` (should be defined in ``<math.h>`` but probably needs to be tested)

doc/sphinx/source/types.rst

@@ -1,17 +0,0 @@
-********
-OBITypes
-********
-
-    
-.. image:: ./UML/OBITypes_UML.png
-:download:`html version of the OBITypes UML file <UML/OBITypes_UML.class.violet.html>`
-
-
-.. toctree::
-   :maxdepth: 2
-
-   The elementary types <elementary>
-   The containers <containers>
-   Special values <specialvalues>
-
-

obi_completion_script.bash

@@ -0,0 +1,25 @@
+
+_obi_comp ()
+{
+	local cur prev
+    cur="${COMP_WORDS[COMP_CWORD]}"
+    prev="${COMP_WORDS[COMP_CWORD-1]}"
+	if [ "${#COMP_WORDS[@]}" = "2" ]; then
+		COMPREPLY=($(compgen -W "align alignpairedend annotate build_ref_db clean_dms clean count ecopcr ecotag export grep head history import less ls ngsfilter sort stats tail test uniq" "${COMP_WORDS[1]}"))
+	else
+		if [[ "$cur" == *VIEWS* ]]; then
+			COMPREPLY=($(compgen -o plusdirs -f -X '!*.obiview' -- "${COMP_WORDS[COMP_CWORD]}"))
+		elif  [[ -d $cur.obidms ]]; then
+			COMPREPLY=($(compgen -o plusdirs -f $cur.obidms/VIEWS/ -- "${COMP_WORDS[COMP_CWORD]}"), $(compgen -o plusdirs -f -X '!*.obidms/' -- "${COMP_WORDS[COMP_CWORD]}"))
+		elif [[ "$cur" == *obidms* ]]; then
+			COMPREPLY=($(compgen -o plusdirs -f $cur/VIEWS/ -- "${COMP_WORDS[COMP_CWORD]}"))
+    	else
+			COMPREPLY=($(compgen -o plusdirs -f -X '!*.obidms/' -- "${COMP_WORDS[COMP_CWORD]}"))
+		fi
+		if [[ "$prev" == import ]]; then
+			COMPREPLY+=($(compgen -f -- "${COMP_WORDS[COMP_CWORD]}"))
+		fi
+	fi
+}
+
+complete -o nospace -F _obi_comp obi

python/.gitignore

@@ -0,0 +1,2 @@
+/.DS_Store
+/OBITools3.egg-info/

python/obitools3/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

python/obitools3/apps/arguments.pxd

@@ -0,0 +1,3 @@
+#cython: language_level=3
+
+cpdef buildArgumentParser(str configname, str softname)

python/obitools3/apps/arguments.pyx

@@ -0,0 +1,58 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import argparse
+import sys
+
+
+from .command import getCommandsList
+
+class ObiParser(argparse.ArgumentParser): 
+    def error(self, message):
+        sys.stderr.write('error: %s\n' % message)
+        self.print_help()
+        sys.exit(2)
+
+cpdef buildArgumentParser(str configname, 
+                          str softname):
+    parser = ObiParser()
+    
+    parser.add_argument('--version',   dest='%s:version' % configname, 
+                                       action='store_true', 
+                                       default=False, 
+                        help='Print the version of %s' % softname)
+
+    parser.add_argument('--log',       dest='%s:log' % configname, 
+                                       action='store',
+                                       type=str,
+                                       default=None, 
+                        help='Create a logfile')
+
+
+    subparsers = parser.add_subparsers(title='subcommands',
+                                       description='valid subcommands',
+                                       help='additional help')
+    
+    commands = getCommandsList()
+    
+    for c in commands:
+        module = commands[c]
+        
+        if hasattr(module, "run"):
+            if hasattr(module, "__title__"):
+                sub = subparsers.add_parser(c,help=module.__title__)
+            else:
+                sub = subparsers.add_parser(c)
+    
+            if hasattr(module, "addOptions"):
+                module.addOptions(sub)
+            
+            sub.set_defaults(**{'%s:module'  % configname : module})
+            sub.set_defaults(**{'%s:modulename'  % configname : c})
+              
+    return parser

python/obitools3/apps/command.pxd

@@ -0,0 +1,3 @@
+#cython: language_level=3
+
+cdef object loadCommand(str name,loader)

python/obitools3/apps/command.pyx

@@ -0,0 +1,44 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import pkgutil
+
+from obitools3 import commands
+
+cdef object loadCommand(str name,loader):
+    '''
+    Load a command module from its name and an ImpLoader
+    
+    This function is for internal use
+    
+    @param name:   name of the module
+    @type name: str 
+    @param loader: the module loader
+    @type loader: ImpLoader
+    
+    @return the loaded module
+    @rtype: module 
+    '''
+    
+    module = loader.find_module(name).load_module(name)
+    return module
+
+def getCommandsList():
+    '''
+    Returns the list of sub-commands available to the main `obi` command
+    
+    @return: a dict instance with key corresponding to each command and
+             value corresponding to the module
+             
+    @rtype: dict
+    '''
+    
+    cdef dict cmds = dict((x[1],loadCommand(x[1],x[0])) 
+                           for x in pkgutil.iter_modules(commands.__path__) 
+                           if not x[2])
+    return cmds

python/obitools3/apps/config.pxd

@@ -0,0 +1,10 @@
+#cython: language_level=3
+
+cpdef str setRootConfigName(str rootname)
+cpdef str getRootConfigName()
+
+cdef dict buildDefaultConfiguration(str root_config_name,
+                                    dict  config)
+
+cpdef dict getConfiguration(str root_config_name=?,
+                                    dict  config=?)

python/obitools3/apps/config.pyx

@@ -0,0 +1,114 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import sys
+
+from .command   import  getCommandsList
+from .logging   cimport getLogger
+from .arguments cimport buildArgumentParser
+
+from ..version import version
+
+
+cdef dict __default_config__ = {}
+
+
+cpdef str setRootConfigName(str rootname):
+    global __default_config__
+    if '__root_config__' in __default_config__:
+        if __default_config__["__root_config__"] in __default_config__:
+            __default_config__[rootname]=__default_config__[__default_config__["__root_config__"]]
+            del __default_config__[__default_config__["__root_config__"]]
+    __default_config__['__root_config__']=rootname
+    return rootname
+
+cpdef str getRootConfigName():
+    global __default_config__
+    return __default_config__.get('__root_config__',None)
+
+cdef dict buildDefaultConfiguration(str root_config_name,
+                                    dict  config):
+    global __default_config__
+    
+    __default_config__.clear()
+    setRootConfigName(root_config_name)    
+
+    __default_config__[root_config_name]=config
+    
+    config['version']=version
+    
+    commands = getCommandsList()
+    
+    for c in commands:
+        module = commands[c]
+    
+        assert hasattr(module, "run")
+        
+        if hasattr(module, 'default_config'):
+            __default_config__[c]=module.default_config
+        else:
+            __default_config__[c]={}
+                        
+    return __default_config__
+        
+
+cpdef dict getConfiguration(str root_config_name="__default__",
+                            dict  config={}):
+    global __default_config__
+
+    if '__done__' in __default_config__:
+        return __default_config__
+    
+    if root_config_name=="__default__":
+        raise RuntimeError("No root_config_name specified")
+    
+    if not config:
+        raise RuntimeError("Base configuration is empty")
+    
+    
+    
+    config =  buildDefaultConfiguration(root_config_name,
+                                        config)
+    
+    parser = buildArgumentParser(root_config_name,
+                                 config[root_config_name]['software'])
+    
+    options = vars(parser.parse_args())
+
+    if options['%s:version' % root_config_name]:
+        print("%s - Version %s" % (config[root_config_name]['software'],
+                                   config[root_config_name]['version']))
+        sys.exit(0)
+    
+    for k in options:
+        section,key = k.split(':')
+        s = config[section]
+        if options[k] is not None:
+            s[key]=options[k]
+            
+    if not 'module' in config[root_config_name]:
+        print('\nError: No command specified',file=sys.stderr)
+        parser.print_help()
+        sys.exit(2)
+                
+    getLogger(config)
+    
+    config['__done__']=True
+            
+    return config
+
+def logger(level, *messages):
+    try:
+        config=getConfiguration()
+        root = config["__root_config__"]
+        l = config[root]['logger']
+        if config[root]['verbose']:
+            getattr(l, level)(*messages)
+    except:
+        print(*messages,file=sys.stderr)
+

python/obitools3/apps/logging.pxd

@@ -0,0 +1,3 @@
+#cython: language_level=3
+
+cpdef getLogger(dict config)

python/obitools3/apps/logging.pyx

@@ -0,0 +1,48 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+import logging
+import sys
+
+cpdef getLogger(dict config):
+    '''
+    Returns the logger as defined by the command line option
+    or by the config file
+    :param config:
+    '''
+    
+    root = config["__root_config__"]
+ 
+    level  = config[root]['loglevel'] 
+    logfile= config[root]['log'] 
+    
+    rootlogger   = logging.getLogger()
+    logFormatter = logging.Formatter("%%(asctime)s [%s : %%(levelname)-5.5s]  %%(message)s" % config[root]['modulename'])
+
+    stderrHandler = logging.StreamHandler(sys.stderr)
+    stderrHandler.setFormatter(logFormatter)
+
+    rootlogger.addHandler(stderrHandler)
+    
+    if logfile:
+        fileHandler = logging.FileHandler(logfile)
+        fileHandler.setFormatter(logFormatter)
+        rootlogger.addHandler(fileHandler)
+    
+    try:
+        loglevel = getattr(logging, level) 
+    except:
+        loglevel = logging.INFO
+        
+    rootlogger.setLevel(loglevel)
+    
+    config[root]['logger']=rootlogger
+    config[root]['verbose']=True
+        
+    return rootlogger
+

python/obitools3/apps/optiongroups/__init__.py

@@ -0,0 +1,389 @@
+import codecs
+
+def unescaped_str(arg_str):
+    return arg_str.encode('latin-1', 'backslashreplace').decode('unicode-escape')
+
+
+def __addInputOption(optionManager):
+    
+    optionManager.add_argument(
+                    dest='obi:inputURI',  
+                    metavar='INPUT', 
+                    help='Data source URI')
+    
+
+    group = optionManager.add_argument_group("Restriction to a sub-part options",
+                    "Allows to limit analysis to a sub-part of the input")
+
+    group.add_argument('--skip',
+                     action="store", dest="obi:skip",
+                     metavar='<N>',
+                     default=None,
+                     type=int,
+                     help="skip the N first sequences")
+
+    group.add_argument('--only',
+                     action="store", dest="obi:only",
+                     metavar='<N>',
+                     default=None,
+                     type=int,
+                     help="treat only N sequences")
+    
+
+def __addImportInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for imported files")
+
+    group.add_argument('--fasta-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'fasta',
+                     help="Input file is in sanger fasta format")
+
+    group.add_argument('--fastq-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'fastq',
+                     help="Input file is in fastq format")
+
+    group.add_argument('--silva-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'silva',
+                     help="Input file is in SILVA fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
+    group.add_argument('--rdp-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'rdp',
+                     help="Input file is in RDP training set fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
+    group.add_argument('--unite-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'unite',
+                     help="Input file is in UNITE fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
+    group.add_argument('--sintax-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'sintax',
+                     help="Input file is in SINTAX fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
+    group.add_argument('--embl-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'embl',
+                     help="Input file is in embl nucleic format")
+
+    group.add_argument('--genbank-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'genbank',
+                     help="Input file is in genbank nucleic format")
+
+    group.add_argument('--ngsfilter-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'ngsfilter',
+                     help="Input file is an ngsfilter file. If not using tags, use ':' or 'None:None' or '-:-' or any combination")
+
+    group.add_argument('--ecopcr-result-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'ecopcr',
+                     help="Input file is the result of an ecoPCR (version 2)")
+
+    group.add_argument('--ecoprimers-result-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'ecoprimers',
+                     help="Input file is the result of an ecoprimers")
+
+    group.add_argument('--tabular-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'tabular',
+                     help="Input file is a tabular file")
+
+    group.add_argument('--no-skip-on-error',
+                     action="store_false", dest="obi:skiperror",
+                     default=True,
+                     help="Don't skip sequence entries with parsing errors (default: they are skipped)")
+
+    group.add_argument('--no-quality',
+                     action="store_true", dest="obi:noquality",
+                     default=False,
+                     help="Do not import fastQ quality")
+
+    group.add_argument('--quality-sanger',
+                     action="store_const", dest="obi:qualityformat",
+                     default=None,
+                     const=b'sanger',
+                     help="Fastq quality is encoded following sanger format (standard fastq)")
+
+    group.add_argument('--quality-solexa',
+                     action="store_const", dest="obi:qualityformat",
+                     default=None,
+                     const=b'solexa',
+                     help="Fastq quality is encoded following solexa sequencer format")
+
+    group.add_argument('--nuc',
+                     action="store_const", dest="obi:moltype",
+                     default=None,
+                     const=b'nuc',
+                     help="Input file contains nucleic sequences")
+    
+    group.add_argument('--prot',
+                     action="store_const", dest="obi:moltype",
+                     default=None,
+                     const=b'pep',
+                     help="Input file contains protein sequences")
+
+    group.add_argument('--input-na-string',
+                     action="store", dest="obi:inputnastring",
+                     default="NA",
+                     type=str,
+                     help="String associated with Non Available (NA) values in the input")
+
+
+def __addTabularOption(optionManager):
+    group = optionManager.add_argument_group("Input and output format options for tabular files")
+
+    group.add_argument('--no-header',
+                     action="store_false", dest="obi:header",
+                     default=True,
+                     help="Don't print the header (first line with column names")
+
+    group.add_argument('--sep',
+                     action="store", dest="obi:sep",
+                     default="\t",
+                     type=unescaped_str,
+                     help="Column separator")
+
+
+def __addTabularInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for tabular files")
+    
+    __addTabularOption(optionManager)
+    
+    group.add_argument('--dec',
+                     action="store", dest="obi:dec",
+                     default=".",
+                     type=str,
+                     help="Decimal separator")
+    
+    group.add_argument('--strip-white',
+                     action="store_false", dest="obi:stripwhite",
+                     default=True,
+                     help="Remove white chars at the beginning and the end of values")
+
+    group.add_argument('--blank-line-skip',
+                     action="store_false", dest="obi:blanklineskip",
+                     default=True,
+                     help="Skip empty lines")
+
+    group.add_argument('--comment-char',
+                     action="store", dest="obi:commentchar",
+                     default="#",
+                     type=str,
+                     help="Lines starting by this char are considered as comment")
+
+
+def __addTabularOutputOption(optionManager):
+    group = optionManager.add_argument_group("Output format options for tabular files")
+    
+    __addTabularOption(optionManager)
+
+    group.add_argument('--na-int-stay-na',
+                     action="store_false", dest="obi:na_int_to_0",
+                     help="NA (Non available) integer values should be exported as NA in tabular output (default: they are converted to 0 for tabular output).") # TODO
+
+
+def __addTaxdumpInputOption(optionManager):  # TODO maybe not the best way to do it
+    group = optionManager.add_argument_group("Input format options for taxdump")
+
+    group.add_argument('--taxdump',
+                     action="store_true", dest="obi:taxdump",
+                     default=False,
+                     help="Whether the input is a taxdump")
+
+
+def __addTaxonomyOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for taxonomy")
+
+    group.add_argument('--taxonomy',
+                     action="store", dest="obi:taxoURI",
+                     default=None,
+                     help="Taxonomy URI")
+    
+    #TODO option bool to download taxo if URI doesn't exist
+
+
+def addMinimalInputOption(optionManager):
+    __addInputOption(optionManager)
+
+    
+def addImportInputOption(optionManager):
+    __addInputOption(optionManager)
+    __addImportInputOption(optionManager)
+
+
+def addTabularInputOption(optionManager):
+    __addTabularInputOption(optionManager)
+
+
+def addTabularOutputOption(optionManager):
+    __addTabularOutputOption(optionManager)
+
+
+def addTaxonomyOption(optionManager):
+    __addTaxonomyOption(optionManager)
+
+
+def addTaxdumpInputOption(optionManager):
+    __addTaxdumpInputOption(optionManager)
+
+
+def addAllInputOption(optionManager):
+    __addInputOption(optionManager)
+    __addImportInputOption(optionManager)
+    __addTabularInputOption(optionManager)
+    __addTabularOutputOption(optionManager)
+    __addTaxonomyOption(optionManager)
+    __addTaxdumpInputOption(optionManager)    
+
+
+def __addOutputOption(optionManager):
+    
+    optionManager.add_argument(
+                    dest='obi:outputURI',
+                    metavar='OUTPUT', 
+                    help='Data destination URI')
+
+
+def __addDMSOutputOption(optionManager):
+    group = optionManager.add_argument_group("Output options for DMS data")
+
+    group.add_argument('--no-create-dms',
+                 action="store_true", dest="obi:nocreatedms",
+                 default=False,
+                 help="Don't create an output DMS if it does not already exist")
+
+
+def __addEltLimitOption(optionManager):
+    group = optionManager.add_argument_group("Option to limit the number of elements per line in columns")
+    group.add_argument('--max-elts',
+                 action="store", dest="obi:maxelts",
+                 metavar='<N>',
+                 default=1000000,
+                 type=int,
+                 help="Maximum number of elements per line in a column "
+                      "(e.g. the number of different keys in a dictionary-type "
+                      "key from sequence headers). If the number of different keys "
+                      "is greater than N, the values are stored as character strings")
+
+
+def __addExportOutputOption(optionManager):
+    group = optionManager.add_argument_group("Output format options for exported files")
+
+    group.add_argument('-o',
+                    dest='obi:outputURI',
+                    metavar='OUTPUT', 
+                    help='Data destination URI')
+
+    group.add_argument('--fasta-output',
+                     action="store_const", dest="obi:outputformat",
+                     default=None,
+                     const=b'fasta',
+                     help="Output file is in sanger fasta format")
+
+    group.add_argument('--fastq-output',
+                     action="store_const", dest="obi:outputformat",
+                     default=None,
+                     const=b'fastq',
+                     help="Output file is in fastq format")
+
+    group.add_argument('--tab-output',
+                     action="store_const", dest="obi:outputformat",
+                     default=None,
+                     const=b'tabular',
+                     help="Output file is in tabular format")
+
+    group.add_argument('--metabaR-output',
+                     action="store_const", dest="obi:outputformat",
+                     default=None,
+                     const=b'metabaR',
+                     help="Export the files needed by the obifiles_to_metabarlist function of the metabaR package")
+
+    group.add_argument('--metabaR-prefix',
+                     action="store", dest="obi:metabarprefix",
+                     type=str,
+                     help="Prefix for the files when using --metabaR-output option")
+
+    group.add_argument('--metabaR-ngsfilter',
+                     action="store", dest="obi:metabarngsfilter",
+                     type=str,
+                     default=None,
+                     help="URI to the ngsfilter view when using --metabaR-output option (if not provided, it is not exported)")
+
+    group.add_argument('--metabaR-samples',
+                     action="store", dest="obi:metabarsamples",
+                     type=str,
+                     default=None,
+                     help="URI to the sample metadata view when using --metabaR-output option (if not provided, it is built as just a list of the sample names)")
+
+    group.add_argument('--only-keys',
+                       action="append", dest="obi:only_keys",
+                       type=str,
+                       default=[],
+                       help="Only export the given keys (columns).")
+
+    group.add_argument('--print-na',
+                     action="store_true", dest="obi:printna",
+                     default=False,
+                     help="Print Non Available (NA) values in the output")
+
+    group.add_argument('--output-na-string',
+                     action="store", dest="obi:outputnastring",
+                     default="NA",
+                     type=str,
+                     help="String associated with Non Available (NA) values in the output")
+
+
+def __addNoProgressBarOption(optionManager):
+    group = optionManager.add_argument_group("Option to deactivate the display of the progress bar")
+
+    group.add_argument('--no-progress-bar',
+                     action="store_true", dest="obi:noprogressbar",
+                     default=False,
+                     help="Do not display progress bar")
+
+
+def addMinimalOutputOption(optionManager):
+    __addOutputOption(optionManager)
+    __addDMSOutputOption(optionManager)
+
+
+def addTabularOutputOption(optionManager):
+    __addTabularOption(optionManager)
+
+
+def addExportOutputOption(optionManager):
+    __addExportOutputOption(optionManager)
+    __addTabularOutputOption(optionManager)
+
+
+def addAllOutputOption(optionManager):
+    __addOutputOption(optionManager)
+    __addDMSOutputOption(optionManager)
+    __addExportOutputOption(optionManager)
+    __addTabularOutputOption(optionManager)
+
+
+def addNoProgressBarOption(optionManager):
+    __addNoProgressBarOption(optionManager)
+    
+def addEltLimitOption(optionManager):
+    __addEltLimitOption(optionManager)
+    
+    

python/obitools3/apps/progress.pxd

@@ -0,0 +1,65 @@
+#cython: language_level=3
+
+cdef extern from "stdio.h":
+    struct FILE
+    int fprintf(FILE *stream, char *format, ...)
+    int fputs(char *string, FILE *stream)
+    FILE* stderr
+    ctypedef unsigned int off_t "unsigned long long"
+    
+cdef extern from "unistd.h":
+    int fsync(int fd);
+
+cdef extern from "time.h":
+    struct tm :
+        int tm_yday 
+        int tm_hour
+        int tm_min
+        int tm_sec
+
+    enum: CLOCKS_PER_SEC
+    
+    ctypedef int time_t
+    ctypedef int clock_t
+    ctypedef int suseconds_t
+    
+    struct timeval:
+        time_t      tv_sec     #  seconds */
+        suseconds_t tv_usec    #  microseconds */
+
+
+    struct timezone :
+        int tz_minuteswest;    # minutes west of Greenwich
+        int tz_dsttime;        # type of DST correction 
+
+        
+    int gettimeofday(timeval *tv, timezone *tz)
+
+
+    tm *gmtime_r(time_t *clock, tm *result)
+    time_t time(time_t *tloc)
+    clock_t clock()
+
+cdef class ProgressBar:
+    cdef off_t   maxi
+    cdef clock_t starttime
+    cdef clock_t lasttime
+    cdef clock_t tickcount
+    cdef int freq
+    cdef int cycle
+    cdef int arrow
+    cdef int lastlog
+    cdef bint ontty
+    cdef int fd
+    cdef bint cut
+    
+    cdef bytes _head
+    cdef char *chead
+    
+    cdef object logger
+
+    cdef char  *wheel
+    cdef char  *spaces
+    cdef char*  diese 
+    
+    cdef clock_t clock(self)

python/obitools3/apps/progress.pyx

@@ -0,0 +1,157 @@
+#cython: language_level=3
+
+'''
+Created on 27 mars 2016
+
+@author: coissac
+'''
+
+
+from ..utils cimport str2bytes, bytes2str
+from .config cimport getConfiguration 
+import sys
+
+
+cdef class ProgressBar:
+    
+    cdef clock_t clock(self):
+        cdef clock_t t
+        cdef timeval tp
+        cdef clock_t s
+        
+        <void> gettimeofday(&tp,NULL)
+        s = <clock_t> (<double> tp.tv_usec * 1.e-6 * <double> CLOCKS_PER_SEC)
+        t = tp.tv_sec * CLOCKS_PER_SEC + s 
+        
+        return t
+
+
+    def __init__(self,
+                 off_t maxi,
+                 dict  config={},
+                 str head="",
+                 double seconds=5,
+                 cut=False):
+        
+        self.starttime = self.clock()
+        self.lasttime  = self.starttime
+        self.tickcount = <clock_t> (seconds * CLOCKS_PER_SEC)
+        self.freq      = 1
+        self.cycle     = 0
+        self.arrow     = 0
+        self.lastlog   = 0
+        
+        if not config:
+            config=getConfiguration()
+        
+        self.ontty = sys.stderr.isatty()
+        
+        if (maxi<=0):
+            maxi=1
+            
+        self.maxi  = maxi
+        self.head  = head
+        self.chead = self._head 
+        self.cut   = cut
+        
+        self.logger=config[config["__root_config__"]]["logger"]
+        self.wheel =  '|/-\\'
+        self.spaces='          ' \
+                    '          ' \
+                    '          ' \
+                    '          ' \
+                    '          '
+        self.diese ='##########' \
+                    '##########' \
+                    '##########' \
+                    '##########' \
+                    '##########'  
+                          
+             
+    def __call__(self, object pos, bint force=False):
+        cdef off_t    ipos
+        cdef clock_t  elapsed
+        cdef clock_t  newtime
+        cdef clock_t  delta
+        cdef clock_t  more 
+        cdef double   percent 
+        cdef tm remain
+        cdef int days,hour,minu,sec
+        cdef off_t fraction
+        cdef int twentyth
+        
+        self.cycle+=1
+    
+        if self.cycle % self.freq == 0 or force:
+            self.cycle=1
+            newtime  = self.clock()
+            delta         = newtime - self.lasttime
+            self.lasttime = newtime
+            elapsed       = newtime - self.starttime
+#            print(" ",delta,elapsed,elapsed/CLOCKS_PER_SEC,self.tickcount)
+            
+            if   delta < self.tickcount / 5 :
+                self.freq*=2
+            elif delta > self.tickcount * 5 and self.freq>1:
+                self.freq/=2
+                
+            
+            if callable(pos):
+                ipos=pos()
+            else:
+                ipos=pos
+                
+            if ipos==0:
+                ipos=1                
+
+            percent = <double>ipos/<double>self.maxi
+            more = <time_t>((<double>elapsed / percent * (1. - percent))/CLOCKS_PER_SEC)
+            <void>gmtime_r(&more, &remain)
+            days  = remain.tm_yday 
+            hour  = remain.tm_hour
+            minu  = remain.tm_min
+            sec   = remain.tm_sec
+                
+            if self.ontty:
+                fraction=<int>(percent * 50.)
+                self.arrow=(self.arrow+1) % 4
+            
+                if days:
+                    <void>fprintf(stderr,b'\r%s %5.1f %% |%.*s%c%.*s] remain : %d days %02d:%02d:%02d\033[K',
+                                    self.chead,
+                                    percent*100,
+                                    fraction,self.diese,
+                                    self.wheel[self.arrow],
+                                    50-fraction,self.spaces,
+                                    days,hour,minu,sec)
+                else:
+                    <void>fprintf(stderr,b'\r%s %5.1f %% |%.*s%c%.*s] remain : %02d:%02d:%02d\033[K',
+                                    self.chead,
+                                    percent*100.,
+                                    fraction,self.diese,
+                                    self.wheel[self.arrow],
+                                    50-fraction,self.spaces,
+                                    hour,minu,sec)
+
+            if self.cut:
+                tenth = int(percent * 10)
+                if tenth != self.lastlog:
+                    
+                    if self.ontty:
+                        <void>fputs(b'\n',stderr)
+                    
+                    self.logger.info('%s %5.1f %% remain : %02d:%02d:%02d\033[K' % (
+                                            bytes2str(self._head),
+                                            percent*100.,
+                                            hour,minu,sec))
+                    self.lastlog=tenth
+        else:
+            self.cycle+=1
+
+
+    property head:    
+        def __get__(self):
+            return self._head
+        def __set__(self,str value):
+            self._head=str2bytes(value)
+            self.chead=self._head

python/obitools3/apps/temp.pxd

@@ -0,0 +1,10 @@
+#cython: language_level=3
+
+'''
+Created on 28 juillet 2017
+
+@author: coissac
+'''
+
+from obitools3.dms.dms cimport DMS
+from obitools3.utils cimport tobytes,tostr

python/obitools3/apps/temp.pyx

@@ -0,0 +1,96 @@
+#cython: language_level=3
+
+'''
+Created on 28 juillet 2017
+
+@author: coissac
+'''
+
+from os import environb,getpid
+from os.path import join, isdir
+from tempfile import TemporaryDirectory, _get_candidate_names
+from shutil import rmtree
+from atexit import register
+
+from obitools3.dms.dms import DMS
+
+from obitools3.apps.config import getConfiguration
+from obitools3.apps.config import logger
+
+cpdef get_temp_dir():
+    """
+    Returns a temporary directory object specific of this instance of obitools.
+    
+    This is an application function. It cannot be called out of an obi command.
+    It requires a valid configuration.
+    
+    If the function is called several time from the same obi session, the same
+    directory is returned.
+    
+    If the OBITMP environment variable exist, the temporary directory is created
+    inside this directory.
+    
+    The directory is automatically destroyed at the end of the end of the process.
+    
+        @return: a temporary python directory object.
+    """
+    cdef bytes tmpdirname
+    cdef dict config = getConfiguration()
+
+    root = config["__root_config__"]
+    
+    try:
+        return config[root]["tempdir"].name
+    except KeyError:
+        pass
+    
+    try:
+        basedir=environb[b'OBITMP']
+    except KeyError:
+        basedir=None
+    
+    tmp = TemporaryDirectory(dir=basedir)
+        
+    config[root]["tempdir"]=tmp
+    
+    return tmp.name
+ 
+cpdef get_temp_dir_name():
+    """
+    Returns the name of the  temporary directory object 
+    specific of this instance of obitools.
+    
+        @return: the name of the temporary directory.
+        
+        @see get_temp_dir
+    """
+    return get_temp_dir_name().name
+          
+               
+cpdef get_temp_dms():
+
+    cdef bytes tmpdirname                   # @DuplicatedSignature
+    cdef dict config = getConfiguration()   # @DuplicatedSignature
+    cdef DMS tmpdms
+    
+    root = config["__root_config__"]
+    
+    try:
+        return config[root]["tempdms"]
+    except KeyError:
+        pass
+
+    tmpdirname=get_temp_dir()
+        
+    tempname = join(tmpdirname,
+                    b"obi.%d.%s" % (getpid(),
+                                    tobytes(next(_get_candidate_names())))
+                   )
+        
+    tmpdms = DMS.new(tempname)
+    
+    config[root]["tempdms"]=tmpdms
+    
+    return tmpdms
+    
+    

python/obitools3/commands/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

python/obitools3/commands/addtaxids.pyx

@@ -0,0 +1,231 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.dms.column.column cimport Column
+from functools import reduce
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes, tostr
+from io import BufferedWriter
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_INT
+from obitools3.dms.capi.obitaxonomy cimport MIN_LOCAL_TAXID
+import time
+import math 
+import sys
+
+from cpython.exc cimport PyErr_CheckSignals
+
+ 
+__title__="Annotate sequences with their corresponding NCBI taxid found from the taxon scientific name"
+
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi addtaxids specific options')
+
+    group.add_argument('-t', '--taxid-tag', 
+                       action="store", 
+                       dest="addtaxids:taxid_tag",
+                       metavar="<TAXID_TAG>",
+                       default=b"TAXID",
+                       help="Name of the tag to store the found taxid "
+                            "(default: 'TAXID').")
+
+    group.add_argument('-n', '--taxon-name-tag', 
+                       action="store", 
+                       dest="addtaxids:taxon_name_tag",
+                       metavar="<SCIENTIFIC_NAME_TAG>",
+                       default=b"SCIENTIFIC_NAME",
+                       help="Name of the tag giving the scientific name of the taxon "
+                            "(default: 'SCIENTIFIC_NAME').")
+
+    group.add_argument('-g', '--try-genus-match',
+                     action="store_true", dest="addtaxids:try_genus_match",
+                     default=False,
+                     help="Try matching the first word of <SCIENTIFIC_NAME_TAG> when can't find corresponding taxid for a taxon. "
+                          "If there is a match it is added in the 'parent_taxid' tag. (Can be used by 'obi taxonomy' to add the taxon under that taxid).")
+
+    group.add_argument('-a', '--restricting-ancestor', 
+                       action="store", 
+                       dest="addtaxids:restricting_ancestor",
+                       metavar="<RESTRICTING_ANCESTOR>",
+                       default=None,
+                       help="Enables to restrict the search of taxids under an ancestor specified by its taxid.")
+
+    group.add_argument('-l', '--log-file', 
+                       action="store", 
+                       dest="addtaxids:log_file",
+                       metavar="<LOG_FILE>",
+                       default='',
+                       help="Path to a log file to write informations about not found taxids.")
+
+
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi addtaxids")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+    i_view_name = input[1].name
+
+    # Open the output: only the DMS, as the output view is going to be created by cloning the input view
+    # (could eventually be done via an open_uri() argument)
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    o_view_name = output[1]
+
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms: # Making sure view name is unique in output DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        imported_view_name = o_view_name
+
+    # If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
+    # (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
+    if i_dms != o_dms:
+        imported_view_name = i_view_name
+        i=0
+        while imported_view_name in o_dms:  # Making sure view name is unique in output DMS
+            imported_view_name = i_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
+        i_view = o_dms[imported_view_name]
+
+    # Clone output view from input view
+    o_view = i_view.clone(o_view_name)
+    if o_view is None:
+        raise Exception("Couldn't create output view")
+    i_view.close()
+
+    # Open taxonomy
+    taxo_uri = open_uri(config['obi']['taxoURI'])
+    if taxo_uri is None or taxo_uri[2] == bytes:
+        raise Exception("Couldn't open taxonomy")
+    taxo = taxo_uri[1]
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(o_view), config)
+    else:
+        pb = None
+        
+    try:
+        if config['addtaxids']['log_file']:
+            logfile = open(config['addtaxids']['log_file'], 'w')
+        else:
+            logfile = None
+        if config['addtaxids']['try_genus_match']:
+            try_genus = True
+        else:
+            try_genus = False
+        if 'restricting_ancestor' in config['addtaxids']:
+            res_anc = int(config['addtaxids']['restricting_ancestor'])
+        else:
+            res_anc = None
+        taxid_column_name = config['addtaxids']['taxid_tag']
+        parent_taxid_column_name = "PARENT_TAXID" # TODO macro
+        taxon_name_column_name = config['addtaxids']['taxon_name_tag']
+        taxid_column = Column.new_column(o_view, taxid_column_name, OBI_INT)
+        parent_taxid_column = Column.new_column(o_view, parent_taxid_column_name, OBI_INT)
+        taxon_name_column = o_view[taxon_name_column_name]
+        
+        found_count = 0
+        not_found_count = 0
+        parent_found_count = 0
+        
+        for i in range(len(o_view)):
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            taxon_name = taxon_name_column[i]
+            taxon = taxo.get_taxon_by_name(taxon_name, res_anc)
+            if taxon is not None:
+                taxid_column[i] = taxon.taxid
+                found_count+=1
+            elif try_genus: # try finding genus or other parent taxon from the first word
+                #print(i, o_view[i].id)
+                taxon_name_sp = taxon_name.split(b" ")
+                taxon = taxo.get_taxon_by_name(taxon_name_sp[0], res_anc)
+                if taxon is not None:
+                    parent_taxid_column[i] = taxon.taxid
+                    parent_found_count+=1
+                    if logfile:
+                        print("Found parent taxon for", tostr(taxon_name), file=logfile)
+                else:
+                    not_found_count+=1
+                    if logfile:
+                        print("No taxid found for", tostr(taxon_name), file=logfile)
+            else:
+                not_found_count+=1
+                if logfile:
+                    print("No taxid found for", tostr(taxon_name), file=logfile)
+
+    except Exception, e:
+        raise RollbackException("obi addtaxids error, rollbacking view: "+str(e), o_view)
+
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+    
+    logger("info", "\nTaxids found: "+str(found_count)+"/"+str(len(o_view))+" ("+str(round(found_count*100.0/len(o_view), 2))+"%)")
+    if config['addtaxids']['try_genus_match']:
+        logger("info", "\nParent taxids found: "+str(parent_found_count)+"/"+str(len(o_view))+" ("+str(round(parent_found_count*100.0/len(o_view), 2))+"%)")
+    logger("info", "\nTaxids not found: "+str(not_found_count)+"/"+str(len(o_view))+" ("+str(round(not_found_count*100.0/len(o_view), 2))+"%)") 
+    
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[input[0].name]
+    input_view_name=[i_view_name]
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+        input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    o_view.write_config(config, "addtaxids", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(o_dms, imported_view_name)
+        o_dms.close(force=True)
+    i_dms.close(force=True)
+
+    logger("info", "Done.")

python/obitools3/commands/align.pxd

@@ -0,0 +1,18 @@
+#cython: language_level=3
+
+
+cpdef align_columns(bytes dms_n, 
+                    bytes input_view_1_n, 
+                    bytes output_view_n,
+                    bytes input_view_2_n=*,
+                    bytes input_column_1_n=*, 
+                    bytes input_column_2_n=*,
+                    bytes input_elt_1_n=*, 
+                    bytes input_elt_2_n=*,
+                    bytes id_column_1_n=*, 
+                    bytes id_column_2_n=*,
+                    double threshold=*, bint normalize=*, 
+                    int reference=*, bint similarity_mode=*,
+                    bint print_seq=*, bint print_count=*,
+                    bytes comments=*,
+                    int thread_count=*)

python/obitools3/commands/align.pyx

@@ -0,0 +1,285 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+
+from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \
+                                            obi_lcs_align_two_columns
+
+from io import BufferedWriter
+from cpython.exc cimport PyErr_CheckSignals
+
+import time
+import sys
+
+
+__title__="Align one sequence column with itself or two sequence columns"
+
+
+def addOptions(parser):
+   
+   addMinimalInputOption(parser)
+   addMinimalOutputOption(parser)
+   addNoProgressBarOption(parser)
+
+   group=parser.add_argument_group('obi align specific options')
+
+   group.add_argument('--input-2', '-I',
+                      action="store", dest="align:inputuri2",
+                      metavar='<INPUT URI>',
+                      default="",
+                      type=str,
+                      help="Eventually, the URI of the second input to align with the first one.")
+      
+   group.add_argument('--threshold','-t',
+                      action="store", dest="align:threshold",
+                      metavar='<THRESHOLD>',
+                      default=0.0,
+                      type=float,
+                      help="Score threshold. If the score is normalized and expressed in similarity (default),"
+                           " it is an identity, e.g. 0.95 for an identity of 95%%. If the score is normalized"
+                           " and expressed in distance, it is (1.0 - identity), e.g. 0.05 for an identity of 95%%."
+                           " If the score is not normalized and expressed in similarity, it is the length of the"
+                           " Longest Common Subsequence. If the score is not normalized and expressed in distance,"
+                           " it is (reference length - LCS length)."
+                           " Only sequence pairs with a similarity above <THRESHOLD> are printed. Default: 0.00"
+                           " (no threshold).")
+   
+   group.add_argument('--longest-length','-L',
+                      action="store_const", dest="align:reflength",
+                      default=0,
+                      const=1,
+                      help="The reference length is the length of the longest sequence."
+                           " Default: the reference length is the length of the alignment.")
+   
+   group.add_argument('--shortest-length','-l',
+                      action="store_const", dest="align:reflength",
+                      default=0,
+                      const=2,
+                      help="The reference length is the length of the shortest sequence."
+                           " Default: the reference length is the length of the alignment.")
+   
+   group.add_argument('--raw','-r',
+                      action="store_false", dest="align:normalize",
+                      default=True,
+                      help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
+   
+   group.add_argument('--distance','-D',
+                      action="store_false", dest="align:similarity",
+                      default=True,
+                      help="Score is expressed in distance. Default: score is expressed in similarity.")
+   
+   group.add_argument('--print-seq','-s',
+                      action="store_true", dest="align:printseq",
+                      default=False,
+                      help="The nucleotide sequences are written in the output view. Default: they are not written.")
+   
+   group.add_argument('--print-count','-n',
+                      action="store_true", dest="align:printcount",
+                      default=False,
+                      help="Sequence counts are written in the output view. Default: they are not written.")
+   
+   group.add_argument('--thread-count','-p',   # TODO should probably be in a specific option group
+                      action="store", dest="align:threadcount",
+                      metavar='<THREAD COUNT>',
+                      default=1,
+                      type=int,
+                      help="Number of threads to use for the computation. Default: one.")
+
+
+cpdef align_columns(bytes dms_n, 
+                    bytes input_view_1_n, 
+                    bytes output_view_n,
+                    bytes input_view_2_n=b"",
+                    bytes input_column_1_n=b"", 
+                    bytes input_column_2_n=b"",
+                    bytes input_elt_1_n=b"", 
+                    bytes input_elt_2_n=b"",
+                    bytes id_column_1_n=b"", 
+                    bytes id_column_2_n=b"",
+                    double threshold=0.0, bint normalize=True, 
+                    int reference=0, bint similarity_mode=True,
+                    bint print_seq=False, bint print_count=False,
+                    bytes comments=b"{}",
+                    int thread_count=1) : 
+
+    if input_view_2_n == b"" and input_column_2_n == b"" :
+        if obi_lcs_align_one_column(dms_n, \
+                                    input_view_1_n, \
+                                    input_column_1_n, \
+                                    input_elt_1_n, \
+                                    id_column_1_n, \
+                                    output_view_n, \
+                                    comments, \
+                                    print_seq, \
+                                    print_count, \
+                                    threshold, normalize, reference, similarity_mode,
+                                    thread_count) < 0 :
+            raise Exception("Error aligning sequences")        
+            
+    else:
+        if obi_lcs_align_two_columns(dms_n, \
+                                     input_view_1_n, \
+                                     input_view_2_n, \
+                                     input_column_1_n, \
+                                     input_column_2_n, \
+                                     input_elt_1_n, \
+                                     input_elt_2_n, \
+                                     id_column_1_n, \
+                                     id_column_2_n, \
+                                     output_view_n, \
+                                     comments, \
+                                     print_seq, \
+                                     print_count, \
+                                     threshold, normalize, reference, similarity_mode) < 0 :
+            raise Exception("Error aligning sequences")        
+ 
+ 
+def run(config):
+    
+    DMS.obi_atexit()
+    
+    logger("info", "obi align")
+
+    # Open the input: only the DMS
+    input = open_uri(config['obi']['inputURI'],
+                     dms_only=True)
+    if input is None:
+        raise Exception("Could not read input")
+    i_dms = input[0]
+    i_dms_name = input[0].name
+    i_uri = input[1]
+    i_view_name = i_uri.split(b"/")[0]
+    i_column_name = b""
+    i_element_name = b""
+    if len(i_uri.split(b"/")) >= 2:
+        i_column_name = i_uri.split(b"/")[1]
+    if len(i_uri.split(b"/")) == 3:
+        i_element_name = i_uri.split(b"/")[2]
+    if len(i_uri.split(b"/")) > 3:
+        raise Exception("Input URI contains too many elements:", config['obi']['inputURI'])
+
+    # Open the second input if there is one
+    i_dms_2 = None
+    i_dms_name_2 = b""
+    original_i_view_name_2 = b""
+    i_view_name_2 = b""
+    i_column_name_2 = b""
+    i_element_name_2 = b""
+    if config['align']['inputuri2']:
+        input_2 = open_uri(config['align']['inputuri2'],
+                           dms_only=True)
+        if input_2 is None:
+            raise Exception("Could not read second input")
+        i_dms_2 = input_2[0]
+        i_dms_name_2 = i_dms_2.name
+        i_uri_2 = input_2[1]
+        original_i_view_name_2 = i_uri_2.split(b"/")[0]
+        if len(i_uri_2.split(b"/")) >= 2:
+            i_column_name_2 = i_uri_2.split(b"/")[1]
+        if len(i_uri_2.split(b"/")) == 3:
+            i_element_name_2 = i_uri_2.split(b"/")[2]
+        if len(i_uri_2.split(b"/")) > 3:
+            raise Exception("Input URI contains too many elements:", config['align']['inputuri2'])
+
+        # If the 2 input DMS are not the same, temporarily import 2nd input view in first input DMS
+        if i_dms != i_dms_2:
+            temp_i_view_name_2 = original_i_view_name_2
+            i=0
+            while temp_i_view_name_2 in i_dms:  # Making sure view name is unique in input DMS
+                temp_i_view_name_2 = original_i_view_name_2+b"_"+str2bytes(str(i))
+                i+=1
+            i_view_name_2 = temp_i_view_name_2
+            View.import_view(i_dms_2.full_path[:-7], i_dms.full_path[:-7], original_i_view_name_2, i_view_name_2)
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output")
+    o_dms = output[0]
+    output_0 = output[0]
+    o_dms_name = o_dms.name 
+    final_o_view_name = output[1]
+    o_view_name = final_o_view_name
+
+    # If stdout output or the input and output DMS are not the same, align creating a temporary view in the input dms that will be exported to 
+    # the right DMS and deleted in the other afterwards.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        
+    # Save command config in View comments
+    command_line = " ".join(sys.argv[1:])
+    
+    i_dms_list = [i_dms_name]
+    if i_dms_name_2:
+        i_dms_list.append(i_dms_name_2)
+    i_view_list = [i_view_name]
+    if original_i_view_name_2:
+        i_view_list.append(original_i_view_name_2)
+    comments = View.print_config(config, "align", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list)
+    
+    # Call cython alignment function
+      # Using default ID columns of the view. TODO discuss adding option
+    align_columns(i_dms.name_with_full_path,  \
+                  i_view_name,  \
+                  o_view_name,  \
+                  input_view_2_n   = i_view_name_2,  \
+                  input_column_1_n = i_column_name,  \
+                  input_column_2_n = i_column_name_2, \
+                  input_elt_1_n    = i_element_name,  \
+                  input_elt_2_n    = i_element_name_2, \
+                  id_column_1_n    = b"",  \
+                  id_column_2_n    = b"", \
+                  threshold        = config['align']['threshold'], \
+                  normalize        = config['align']['normalize'],  \
+                  reference        = config['align']['reflength'],  \
+                  similarity_mode  = config['align']['similarity'],  \
+                  print_seq        = config['align']['printseq'],  \
+                  print_count      = config['align']['printcount'], \
+                  comments         = comments, \
+                  thread_count     = config['align']['threadcount'])
+
+    # If the input and output DMS are not the same, export result view to output DMS
+    if i_dms != o_dms:
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+
+    # Save command config in output DMS comments
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
+
+    # If the two input DMS are different, delete the temporary input view in the first input DMS
+    if i_dms_2 and i_dms != i_dms_2:
+        View.delete_view(i_dms, i_view_name_2)
+        i_dms_2.close()
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If the input and the output DMS are different, delete the temporary result view in the input DMS
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close(force=True)
+    
+    i_dms.close(force=True)
+    
+    logger("info", "Done.")
+  

python/obitools3/commands/alignpairedend.pxd

@@ -0,0 +1,4 @@
+#cython: language_level=3
+
+
+cdef object buildAlignment(object direct, object reverse)

python/obitools3/commands/alignpairedend.pyx

@@ -0,0 +1,293 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+from obitools3.dms.column.column cimport Column
+from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_QUAL
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.libalign._qsassemble import QSolexaReverseAssemble
+from obitools3.libalign._qsrassemble import QSolexaRightReverseAssemble
+from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequence
+from obitools3.dms.obiseq cimport Nuc_Seq
+from obitools3.libalign.shifted_ali cimport Kmer_similarity, Ali_shifted
+from obitools3.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
+from obitools3.utils cimport str2bytes
+
+from io import BufferedWriter
+import sys
+import os
+
+from cpython.exc cimport PyErr_CheckSignals
+
+__title__="Align paired-ended reads"
+
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+ 
+    group = parser.add_argument_group('obi alignpairedend specific options')
+
+    group.add_argument('-R', '--reverse-reads',
+                     action="store", dest="alignpairedend:reverse",
+                     metavar="<URI>",
+                     default=None,
+                     type=str,
+                     help="URI to the reverse reads if they are in a different view than the forward reads")
+
+#     group.add_argument('--score-min',
+#                      action="store", dest="alignpairedend:smin",
+#                      metavar="#.###",
+#                      default=None,
+#                      type=float,
+#                      help="Minimum score for keeping alignments. " 
+#                           "(for kmer alignment) The score is an approximation of the number of nucleotides matching in the overlap of the alignment.")
+
+#     group.add_argument('-A', '--true-ali',
+#                        action="store_true", dest="alignpairedend:trueali",
+#                        default=False,
+#                        help="Performs gap free end alignment of sequences instead of using kmers to compute alignments (slower).")
+
+    group.add_argument('-k', '--kmer-size',
+                       action="store", dest="alignpairedend:kmersize",
+                       metavar="#",
+                       default=3,
+                       type=int,
+                       help="K-mer size for kmer comparisons, between 1 and 4 (default: 3)")
+
+
+la = QSolexaReverseAssemble()
+ra = QSolexaRightReverseAssemble()
+cdef object buildAlignment(object direct, object reverse):
+    
+    if len(direct)==0 or len(reverse)==0:
+        return None
+    
+    la.seqA = direct
+    la.seqB = reverse
+    
+    ali=la()
+    ali.direction='left'
+
+    ra.seqA = direct
+    ra.seqB = reverse
+
+    rali=ra()
+    rali.direction='right'
+     
+    if ali.score < rali.score:
+        ali = rali
+    
+    return ali
+    
+
+def alignmentIterator(entries, aligner): 
+    
+    if type(entries) == list:
+        two_views = True
+        forward = entries[0]
+        reverse = entries[1]
+        entries_len = len(forward)
+    else:
+        two_views = False
+        entries_len = len(entries)
+    
+    for i in range(entries_len):
+                
+        if two_views:
+            seqF = forward[i]
+            seqR = reverse[i]
+        else:
+            seqF = Nuc_Seq.new_from_stored(entries[i])
+            seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQUENCE_COLUMN], quality=seqF[REVERSE_QUALITY_COLUMN])
+            seqR.index = i
+        
+        ali = aligner(seqF, seqR)
+        
+        if ali is None:
+            continue
+        
+        yield ali
+
+
+def run(config):
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi alignpairedend")
+       
+    # Open the input
+    
+    two_views = False
+    forward = None
+    reverse = None
+    input = None
+    
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not open input reads")
+    if input[2] != View_NUC_SEQS:
+        raise NotImplementedError('obi alignpairedend only works on NUC_SEQS views')    
+    
+    if "reverse" in config["alignpairedend"]:
+        
+        two_views = True
+        
+        forward = input[1]        
+        
+        rinput = open_uri(config["alignpairedend"]["reverse"])
+        if rinput is None:
+            raise Exception("Could not open reverse reads")
+        if rinput[2] != View_NUC_SEQS:
+            raise NotImplementedError('obi alignpairedend only works on NUC_SEQS views')
+        
+        reverse = rinput[1]
+    
+        if len(forward) != len(reverse):
+            raise Exception("Error: the number of forward and reverse reads are different")
+        
+        entries = [forward, reverse]
+        input_dms_name = [forward.dms.name, reverse.dms.name]
+        input_view_name = [forward.name, reverse.name]
+    
+    else:
+        entries = input[1]
+        input_dms_name = [entries.dms.name]
+        input_view_name = [entries.name]
+
+    if two_views:
+        entries_len = len(forward)
+    else:
+        entries_len = len(entries)
+    
+    # Open the output
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      newviewtype=View_NUC_SEQS)
+    if output is None:
+        raise Exception("Could not create output view")
+
+    output_0 = output[0]
+    o_dms = output[0]
+    
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        i_dms = forward.dms   # using any dms
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view = View_NUC_SEQS.new(o_dms, o_view_name, quality=True)
+    else:
+        o_view = output[1]
+        Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL)
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(entries_len, config)
+    else:
+        pb = None
+         
+    #if config['alignpairedend']['trueali']:
+    #    kmer_ali = False
+    #    aligner = buildAlignment
+    #else :
+    kmer_ali = True
+    if type(entries) == list:
+        forward = entries[0]
+        reverse = entries[1]
+        if len(forward) == 0 or len(reverse) == 0:
+            aligner = None
+        else:
+            aligner = Kmer_similarity(forward, \
+                                      view2=reverse, \
+                                      kmer_size=config['alignpairedend']['kmersize'], \
+                                      reversed_column=None)
+    else:
+        if len(entries) == 0:
+            aligner = None
+        else:
+            aligner = Kmer_similarity(entries, \
+                                      column2=entries[REVERSE_SEQUENCE_COLUMN], \
+                                      qual_column2=entries[REVERSE_QUALITY_COLUMN], \
+                                      kmer_size=config['alignpairedend']['kmersize'], \
+                                      reversed_column=entries[b'reversed'])  # column created by the ngsfilter tool
+        
+    ba = alignmentIterator(entries, aligner)
+    
+    i = 0
+    for ali in ba:
+        
+        if pb is not None:
+            pb(i)
+        
+        PyErr_CheckSignals()
+
+        consensus = o_view[i]
+        
+        if two_views:
+            consensus[b"R1_parent"] = forward[i].id
+            consensus[b"R2_parent"] = reverse[i].id
+               
+        if not two_views:
+            seqF = entries[i]
+        else:
+            seqF = forward[i]
+                        
+        if ali.overlap_len > 0 :
+            buildConsensus(ali, consensus, seqF)
+        else:
+            if not two_views:
+                seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQUENCE_COLUMN], quality = seqF[REVERSE_QUALITY_COLUMN])
+            else:
+                seqR = reverse[i]
+            buildJoinedSequence(ali, seqR, consensus, forward=seqF)
+                   
+        if kmer_ali :
+            ali.free()
+    
+        i+=1
+
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+
+    if kmer_ali and aligner is not None:
+        aligner.free()
+
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(view), file=sys.stderr)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If stdout output, delete the temporary imported view used to create the final file
+    if type(output_0)==BufferedWriter:
+        View_NUC_SEQS.delete_view(o_dms, o_view_name)
+        output_0.close()
+
+    # Close all DMS
+    input[0].close(force=True)
+    if two_views:
+        rinput[0].close(force=True)
+    o_dms.close(force=True)
+
+    logger("info", "Done.")
+    

python/obitools3/commands/annotate.pyx

@@ -0,0 +1,405 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from functools import reduce
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+from io import BufferedWriter
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_STR
+from obitools3.dms.column.column cimport Column
+
+import time
+import math 
+import sys
+
+from cpython.exc cimport PyErr_CheckSignals
+
+ 
+__title__="Annotate views with new tags and edit existing annotations"
+
+
+SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi annotate specific options')
+ 
+    group.add_argument('--seq-rank',   # TODO seq/elt/line???
+                       action="store_true", 
+                       dest="annotate:add_rank",
+                       default=False,
+                       help="Add a rank attribute to the sequence "
+                            "indicating the sequence position in the data.")
+ 
+    group.add_argument('-R', '--rename-tag',
+                       action="append", 
+                       dest="annotate:rename_tags",
+                       metavar="<OLD_NAME:NEW_NAME>",
+                       type=str,
+                       default=[],
+                       help="Change tag name from OLD_NAME to NEW_NAME.")
+
+    group.add_argument('-D', '--delete-tag',
+                       action="append", 
+                       dest="annotate:delete_tags",
+                       metavar="<TAG_NAME>",
+                       type=str,
+                       default=[],
+                       help="Delete tag TAG_NAME.")
+
+    group.add_argument('-S', '--set-tag',
+                       action="append", 
+                       dest="annotate:set_tags",
+                       metavar="<TAG_NAME:PYTHON_EXPRESSION>",
+                       type=str,
+                       default=[],
+                       help="Add a new tag named TAG_NAME with "
+                            "a value computed from PYTHON_EXPRESSION.")
+
+    group.add_argument('--set-identifier',
+                       action="store", 
+                       dest="annotate:set_identifier",
+                       metavar="<PYTHON_EXPRESSION>",
+                       type=str,
+                       default=None,
+                       help="Set sequence identifier with "
+                            "a value computed from PYTHON_EXPRESSION.")
+    
+    group.add_argument('--set-sequence',
+                       action="store", 
+                       dest="annotate:set_sequence",
+                       metavar="<PYTHON_EXPRESSION>",
+                       type=str,
+                       default=None,
+                       help="Change the sequence itself with "
+                            "a value computed from PYTHON_EXPRESSION.")
+
+    group.add_argument('--set-definition',
+                       action="store", 
+                       dest="annotate:set_definition",
+                       metavar="<PYTHON_EXPRESSION>",
+                       type=str,
+                       default=None,
+                       help="Set sequence definition with "
+                            "a value computed from PYTHON_EXPRESSION.")
+
+    group.add_argument('--run',
+                       action="store", 
+                       dest="annotate:run",
+                       metavar="<PYTHON_EXPRESSION>",
+                       type=str,
+                       default=None,
+                       help="Run a python expression on each element.")
+
+    group.add_argument('-C', '--clear',
+                       action="store_true", 
+                       dest="annotate:clear",
+                       default=False,
+                       help="Clear all tags except the obligatory ones.")
+    
+    group.add_argument('-k','--keep',
+                       action='append',
+                       dest="annotate:keep",
+                       metavar="<TAG>",
+                       default=[],
+                       type=str,
+                       help="Only keep this tag. (Can be specified several times.)")
+    
+    group.add_argument('--length',
+                       action="store_true", 
+                       dest="annotate:length",
+                       default=False,
+                       help="Add 'seq_length' tag with sequence length.")
+    
+    group.add_argument('--with-taxon-at-rank',
+                       action='append',
+                       dest="annotate:taxon_at_rank",
+                       metavar="<RANK_NAME>",
+                       default=[],
+                       type=str,
+                       help="Add taxonomy annotation at the specified rank level RANK_NAME.")
+
+
+def sequenceTaggerGenerator(config, taxo=None):
+    
+    toSet=None
+    newId=None
+    newDef=None
+    newSeq=None
+    length=None
+    add_rank=None
+    run=None
+    
+    if 'set_tags' in config['annotate']:   # TODO default option problem, to fix
+        toSet = [x.split(':',1) for x in config['annotate']['set_tags'] if len(x.split(':',1))==2]
+    if 'set_identifier' in config['annotate']:
+        newId = config['annotate']['set_identifier']
+    if 'set_definition' in config['annotate']:
+        newDef = config['annotate']['set_definition']
+    if 'set_sequence' in config['annotate']:
+        newSeq = config['annotate']['set_sequence']
+    if 'length' in config['annotate']:
+        length = config['annotate']['length']
+    if 'add_rank' in config["annotate"]:
+        add_rank = config["annotate"]["add_rank"]
+    if 'run' in config['annotate']:
+        run = config['annotate']['run']
+    counter = [0]
+    
+    for i in range(len(toSet)):
+        for j in range(len(toSet[i])):
+            toSet[i][j] = tobytes(toSet[i][j])
+
+    annoteRank=[]
+    if config['annotate']['taxon_at_rank']:
+        if taxo is not None:
+            annoteRank = config['annotate']['taxon_at_rank']
+        else:
+            raise Exception("A taxonomy must be provided to annotate taxon ranks")
+    
+    def sequenceTagger(seq):
+                
+        if counter[0]>=0:
+            counter[0]+=1
+                            
+        for rank in annoteRank:
+            if TAXID_COLUMN in seq:
+                taxid = seq[TAXID_COLUMN]
+                if taxid is not None:
+                    rtaxid = taxo.get_taxon_at_rank(taxid, rank)
+                    if rtaxid is not None:
+                        scn = taxo.get_scientific_name(rtaxid)
+                    else:
+                        scn=None
+                    seq[rank]=rtaxid
+                    if "%s_name"%rank not in seq.view:
+                        Column.new_column(seq.view, "%s_name"%rank, OBI_STR)
+                    seq["%s_name"%rank]=scn
+             
+        if add_rank:
+            seq['seq_rank']=counter[0]
+    
+        for i,v in toSet:
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}
+                val = eval(v, environ, seq)
+            except Exception:       # set string if not a valid expression
+                val = v
+            seq[i]=val
+
+        if length:
+            seq['seq_length']=len(seq)
+
+        if newId is not None:
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newId, environ, seq)
+            except Exception:      # set string if not a valid expression
+                val = newId
+            seq.id=val
+
+        if newDef is not None:
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newDef, environ, seq)
+            except Exception:    # set string if not a valid expression
+                val = newDef
+            seq.definition=val
+             
+        if newSeq is not None:
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newSeq, environ, seq)
+            except Exception:    # set string if not a valid expression
+                val = newSeq
+            seq.seq=val
+            if 'seq_length' in seq:
+                seq['seq_length']=len(seq)
+            # Delete quality since it must match the sequence.
+            # TODO discuss deleting for each sequence separately
+            if QUALITY_COLUMN in seq:
+                seq.view.delete_column(QUALITY_COLUMN)
+                    
+        if run is not None:
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                eval(run, environ, seq)
+            except Exception,e:
+                raise e
+
+    return sequenceTagger
+
+
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi annotate")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+    i_view_name = input[1].name
+
+    # Open the output: only the DMS, as the output view is going to be created by cloning the input view
+    # (could eventually be done via an open_uri() argument)
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    o_view_name = output[1]
+
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms: # Making sure view name is unique in output DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        imported_view_name = o_view_name
+
+    # If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
+    # (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
+    if i_dms != o_dms:
+        imported_view_name = i_view_name
+        i=0
+        while imported_view_name in o_dms:  # Making sure view name is unique in output DMS
+            imported_view_name = i_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
+        i_view = o_dms[imported_view_name]
+
+    # Clone output view from input view
+    o_view = i_view.clone(o_view_name)
+    if o_view is None:
+        raise Exception("Couldn't create output view")
+    i_view.close()
+
+    # Open taxonomy if there is one
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        taxo_uri = open_uri(config['obi']['taxoURI'])
+        if taxo_uri is None or taxo_uri[2] == bytes:
+            raise Exception("Couldn't open taxonomy")
+        taxo = taxo_uri[1]
+    else :
+        taxo = None
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(o_view), config)
+    else:
+        pb = None
+
+    try:
+
+        # Apply editions
+        # Editions at view level
+        if 'delete_tags' in config['annotate']:
+            toDelete = config['annotate']['delete_tags'][:]
+        if 'rename_tags' in config['annotate']:
+            toRename = [x.split(':',1) for x in config['annotate']['rename_tags'] if len(x.split(':',1))==2]
+        if 'clear' in config['annotate']:
+            clear = config['annotate']['clear']
+        if 'keep' in config['annotate']:
+            keep = config['annotate']['keep']
+        for i in range(len(toDelete)):
+            toDelete[i] = tobytes(toDelete[i])
+        for i in range(len(toRename)):
+            for j in range(len(toRename[i])):
+                toRename[i][j] = tobytes(toRename[i][j])
+        for i in range(len(keep)):
+            keep[i] = tobytes(keep[i])
+        keep = set(keep)
+    
+        if clear or keep:
+            keys = [k for k in o_view.keys()]
+            for k in keys:
+                if k not in keep and k not in SPECIAL_COLUMNS:
+                    o_view.delete_column(k)
+        else:
+            for k in toDelete:
+                o_view.delete_column(k)
+            for old_name, new_name in toRename:
+                if old_name in o_view:
+                    o_view.rename_column(old_name, new_name)
+        
+        # Editions at line level
+        sequenceTagger = sequenceTaggerGenerator(config, taxo=taxo)
+        for i in range(len(o_view)):
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            sequenceTagger(o_view[i])
+
+    except Exception, e:
+        raise RollbackException("obi annotate error, rollbacking view: "+str(e), o_view)
+
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+    
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[input[0].name]
+    input_view_name=[i_view_name]
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+        input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    o_view.write_config(config, "annotate", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(o_dms, imported_view_name)
+        o_dms.close(force=True)
+    i_dms.close(force=True)
+
+    logger("info", "Done.")

python/obitools3/commands/build_ref_db.pyx

@@ -0,0 +1,117 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms.dms cimport DMS
+from obitools3.dms.view import RollbackException
+from obitools3.dms.capi.build_reference_db cimport build_reference_db
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+from obitools3.dms.view.view cimport View
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+
+from io import BufferedWriter
+import sys
+from cpython.exc cimport PyErr_CheckSignals
+
+
+__title__="Build a reference database for ecotag"
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+ 
+    group = parser.add_argument_group('obi build_ref_db specific options')
+
+    group.add_argument('--threshold','-t',
+                      action="store", dest="build_ref_db:threshold",
+                      metavar='<THRESHOLD>',
+                      default=0.99,
+                      type=float,
+                      help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.99.")
+
+
+def run(config):
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi build_ref_db")
+
+    # Open the input: only the DMS
+    input = open_uri(config['obi']['inputURI'],
+                     dms_only=True)
+    if input is None:
+        raise Exception("Could not read input")
+    i_dms = input[0]
+    i_dms_name = input[0].name
+    i_view_name = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output")
+    o_dms = output[0]
+    output_0 = output[0]
+    final_o_view_name = output[1]
+    
+    # If stdout output or the input and output DMS are not the same, build the database creating a temporary view that will be exported to 
+    # the right DMS and deleted in the other afterwards.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
+
+    # Read taxonomy name
+    taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
+
+    # Save command config in View comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[i_dms_name]
+    input_view_name= [i_view_name]
+    input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+    input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    
+    if build_reference_db(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
+        raise Exception("Error building a reference database")
+    
+    # If the input and output DMS are not the same, export result view to output DMS
+    if i_dms != o_dms:
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # Save command config in DMS comments
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close(force=True)
+    
+    i_dms.close(force=True)
+
+    logger("info", "Done.")
+    

python/obitools3/commands/cat.pyx

@@ -0,0 +1,168 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+from obitools3.dms.view.view cimport View
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, REVERSE_SEQUENCE_COLUMN, \
+                                        QUALITY_COLUMN, REVERSE_QUALITY_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
+from obitools3.dms.column.column cimport Column
+
+from io import BufferedWriter
+import time
+import sys
+ 
+from cpython.exc cimport PyErr_CheckSignals
+
+
+__title__="Concatenate views"
+
+ 
+def addOptions(parser):
+    
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi cat specific options')
+
+    group.add_argument("-c",
+                       action="append", dest="cat:views_to_cat",
+                       metavar="<VIEW_NAME>",
+                       default=[],
+                       type=str,
+                       help="URI of a view to concatenate. (e.g. 'my_dms/my_view'). "
+                            "Several -c options can be used on the same "
+                            "command line.")
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi cat")
+
+    # Check the views to concatenate
+    idms_list = []
+    iview_list = []
+    total_len = 0
+    remove_qual = False
+    remove_rev_qual = False
+    v_type = View_NUC_SEQS
+    for v_uri in config["cat"]["views_to_cat"]:
+        input = open_uri(v_uri)
+        if input is None:
+            raise Exception("Could not read input view")
+        i_dms = input[0]
+        i_view = input[1]
+        if input[2] != View_NUC_SEQS:  # Check view type (output view is nuc_seqs view if all input view are nuc_seqs view)
+            v_type = View
+        if QUALITY_COLUMN not in i_view: # Check if keep quality column in output view (if all input views have it)
+            remove_qual = True
+        if REVERSE_QUALITY_COLUMN not in i_view: # same as above for reverse quality
+            remove_rev_qual = True
+        total_len += len(i_view)
+        idms_list.append(i_dms)
+        iview_list.append(i_view.name)
+        i_view.close()
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False, 
+                      newviewtype=v_type)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    o_view = output[1]
+    
+    # stdout output
+    if type(output_0)==BufferedWriter: 
+        o_dms = i_dms
+    
+    # Initialize quality columns and their associated sequence columns if needed
+    if type(output_0) != BufferedWriter: 
+        if not remove_qual:
+            if NUC_SEQUENCE_COLUMN not in o_view:
+                Column.new_column(o_view, NUC_SEQUENCE_COLUMN, OBI_SEQ)
+            Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL, associated_column_name=NUC_SEQUENCE_COLUMN, associated_column_version=o_view[NUC_SEQUENCE_COLUMN].version)    
+        if not remove_rev_qual:
+            Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
+            Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
+        
+    # Initialize multiple elements columns
+    if type(output_0)!=BufferedWriter: 
+        dict_cols = {}
+        for v_uri in config["cat"]["views_to_cat"]:
+            v = open_uri(v_uri)[1]
+            for coln in v.keys():
+                col = v[coln]
+                if v[coln].nb_elements_per_line > 1:
+                    if coln not in dict_cols:
+                        dict_cols[coln] = {}
+                        dict_cols[coln]['eltnames'] = set(v[coln].elements_names)
+                        dict_cols[coln]['nbelts'] = v[coln].nb_elements_per_line
+                        dict_cols[coln]['obitype'] = v[coln].data_type_int
+                    else:
+                        dict_cols[coln]['eltnames'] = set(v[coln].elements_names + list(dict_cols[coln]['eltnames']))
+                        dict_cols[coln]['nbelts'] = len(dict_cols[coln]['eltnames'])
+            v.close()            
+        for coln in dict_cols:
+            Column.new_column(o_view, coln, dict_cols[coln]['obitype'], 
+                              nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']), dict_column=True)
+    
+    # Initialize the progress bar
+    if not config['obi']['noprogressbar']:
+        pb = ProgressBar(total_len, config)
+    else:
+        pb = None
+    
+    i = 0
+    for v_uri in config["cat"]["views_to_cat"]:
+        v = open_uri(v_uri)[1]
+        for entry in v:
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            if type(output_0)==BufferedWriter: 
+                rep = repr(entry)
+                output_0.write(str2bytes(rep)+b"\n")
+            else:
+                try:
+                    o_view[i] = entry
+                except:
+                    print("\nError with entry:", repr(entry))
+                    print(repr(o_view))
+            i+=1
+        v.close()
+
+    # Deletes quality columns if needed
+    if type(output_0)!=BufferedWriter: 
+        if QUALITY_COLUMN in o_view and remove_qual :
+            o_view.delete_column(QUALITY_COLUMN)
+        if REVERSE_QUALITY_COLUMN in o_view and remove_rev_qual :
+            o_view.delete_column(REVERSE_QUALITY_COLUMN)
+    
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+    
+    # Save command config in DMS comments
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "cat", command_line, input_dms_name=[d.name for d in idms_list], input_view_name=[vname for vname in iview_list])
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(view), file=sys.stderr)
+
+    for d in idms_list:
+        d.close(force=True)
+    o_dms.close(force=True)
+    
+    logger("info", "Done.")

python/obitools3/commands/clean.pyx

@@ -0,0 +1,146 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms.dms cimport DMS
+from obitools3.dms.view import RollbackException
+from obitools3.dms.capi.obiclean cimport obi_clean
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+from obitools3.dms.view.view cimport View
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+
+from io import BufferedWriter
+import sys
+
+
+__title__="Tag a set of sequences for PCR and sequencing errors identification"
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+    
+    group = parser.add_argument_group('obi clean specific options')
+
+    group.add_argument('--distance', '-d',
+                       action="store", dest="clean:distance",
+                       metavar='<DISTANCE>',
+                       default=1.0,
+                       type=float,
+                       help="Maximum numbers of errors between two variant sequences. Default: 1.")
+
+    group.add_argument('--sample-tag', '-s',
+                       action="store", 
+                       dest="clean:sample-tag-name",
+                       metavar="<SAMPLE TAG NAME>",
+                       type=str,
+                       help="Name of the tag where merged sample count informations are kept (typically generated by obi uniq, usually MERGED_sample, default: None).")
+    
+    group.add_argument('--ratio', '-r',
+                       action="store", dest="clean:ratio",
+                       metavar='<RATIO>',
+                       default=0.5,
+                       type=float,
+                       help="Maximum ratio between the counts of two sequences so that the less abundant one can be considered"
+                            " a variant of the more abundant one. Default: 0.5.")
+ 
+    group.add_argument('--heads-only', '-H',
+                       action="store_true", 
+                       dest="clean:heads-only",
+                       default=False,
+                       help="Only sequences labeled as heads are kept in the output. Default: False")
+
+#    group.add_argument('--cluster-tags', '-C',
+#                       action="store_true", 
+#                       dest="clean:cluster-tags",
+#                       default=False,
+#                       help="Adds tags for each sequence giving its cluster's head and weight for each sample.")
+
+    group.add_argument('--thread-count','-p',   # TODO should probably be in a specific option group
+                       action="store", dest="clean:thread-count",
+                       metavar='<THREAD COUNT>',
+                       default=-1,
+                       type=int,
+                       help="Number of threads to use for the computation. Default: the maximum available.")
+
+
+def run(config):
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi clean")
+
+    # Open the input: only the DMS
+    input = open_uri(config['obi']['inputURI'],
+                     dms_only=True)
+    if input is None:
+        raise Exception("Could not read input")
+    i_dms = input[0]
+    i_dms_name = input[0].name
+    i_view_name = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output")
+    o_dms = output[0]
+    output_0 = output[0]
+    final_o_view_name = output[1]
+    
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported to 
+    # the right DMS and deleted in the other afterwards.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
+        
+    # Save command config in View comments
+    command_line = " ".join(sys.argv[1:])
+    comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
+
+    if 'sample-tag-name' not in config['clean']:
+        config['clean']['sample-tag-name'] = ""
+        
+    if obi_clean(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
+              config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], config['clean']['thread-count']) < 0:
+        raise Exception("Error running obiclean")
+    
+    # If the input and output DMS are not the same, export result view to output DMS
+    if i_dms != o_dms:
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # Save command config in DMS comments
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close(force=True)
+    
+    i_dms.close(force=True)
+
+    logger("info", "Done.")
+    

python/obitools3/commands/clean_dms.pyx

@@ -0,0 +1,30 @@
+#cython: language_level=3
+
+from obitools3.apps.optiongroups import addMinimalInputOption
+from obitools3.uri.decode import open_uri
+from obitools3.dms import DMS
+from obitools3.dms.capi.obidms cimport obi_clean_dms
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes
+
+ 
+__title__="Clean a DMS from unfinished views and columns"
+ 
+
+def addOptions(parser):
+    addMinimalInputOption(parser)
+  
+
+def run(config):
+    
+    DMS.obi_atexit()
+    
+    logger("info", "obi clean_dms")
+    
+    dms_path = tobytes(config['obi']['inputURI'])
+    if b'.obidms' in dms_path:
+        dms_path = dms_path.split(b'.obidms')[0]
+    if obi_clean_dms(dms_path) < 0 :
+        raise Exception("Error cleaning DMS", config['obi']['inputURI'])
+
+    logger("info", "Done.")

python/obitools3/commands/count.pyx

@@ -0,0 +1,68 @@
+#cython: language_level=3
+
+
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.dms import DMS
+from obitools3.apps.optiongroups import addMinimalInputOption
+from obitools3.dms.capi.obiview cimport COUNT_COLUMN
+
+from cpython.exc cimport PyErr_CheckSignals
+
+
+__title__="Count sequence records"
+
+ 
+def addOptions(parser):
+ 
+    addMinimalInputOption(parser)
+ 
+    group = parser.add_argument_group('obi count specific options')
+ 
+    group.add_argument('-s','--sequence',
+                        action="store_true", dest="count:sequence",
+                        default=False,
+                        help="Prints only the number of sequence records (much faster, default: False).")
+ 
+    group.add_argument('-a','--all',
+                        action="store_true", dest="count:all",
+                        default=False,
+                        help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False).")
+
+    group.add_argument('-c','--count-tag',
+                        action="store", dest="count:countcol",
+                        default='COUNT',
+                        type=str,
+                        help="Name of the tag/column associated with the count information (default: COUNT).")
+
+    
+def run(config):
+    
+    DMS.obi_atexit()
+    
+    logger("info", "obi count")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input")
+    entries = input[1]
+    
+    countcol = config['count']['countcol'] 
+    
+    count1 = len(entries)
+    count2 = 0
+    
+    if countcol in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
+        for e in entries:
+            PyErr_CheckSignals()
+            count2+=e[countcol]
+
+    if countcol in entries and (config['count']['sequence'] == config['count']['all']):
+        print(count1,count2)
+    elif countcol in entries and config['count']['all']:
+        print(count2)
+    else:
+        print(count1)
+    
+    input[0].close(force=True)

python/obitools3/commands/ecopcr.pyx

@@ -0,0 +1,242 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms.dms cimport DMS
+from obitools3.dms.capi.obidms cimport OBIDMS_p
+from obitools3.dms.view import RollbackException
+from obitools3.dms.capi.obiecopcr cimport obi_ecopcr
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addTaxonomyOption, addNoProgressBarOption
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+from obitools3.dms.view import View
+
+from libc.stdlib  cimport malloc, free
+from libc.stdint  cimport int32_t
+
+import sys
+from io import BufferedWriter
+
+
+__title__="in silico PCR"
+
+
+# TODO: add option to output unique ids
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+ 
+    group = parser.add_argument_group('obi ecopcr specific options')
+
+    group.add_argument('--primer1', '-F',
+                       action="store", dest="ecopcr:primer1",
+                       metavar='<PRIMER>',
+                       type=str,
+                       required=True,
+                       help="Forward primer, length must be less than or equal to 32")
+
+    group.add_argument('--primer2', '-R',
+                       action="store", dest="ecopcr:primer2",
+                       metavar='<PRIMER>',
+                       type=str,
+                       required=True,
+                       help="Reverse primer, length must be less than or equal to 32")
+
+    group.add_argument('--error', '-e',
+                       action="store", dest="ecopcr:error",
+                       metavar='<ERROR>',
+                       default=0,
+                       type=int,
+                       help="Maximum number of errors (mismatches) allowed per primer. Default: 0.")
+
+    group.add_argument('--min-length', '-l',
+                       action="store", 
+                       dest="ecopcr:min-length",
+                       metavar="<MINIMUM LENGTH>",
+                       type=int,
+                       default=0,
+                       help="Minimum length of the in silico amplified DNA fragment, excluding primers.")
+    
+    group.add_argument('--max-length', '-L',
+                       action="store", 
+                       dest="ecopcr:max-length",
+                       metavar="<MAXIMUM LENGTH>",
+                       type=int,
+                       default=0,
+                       help="Maximum length of the in silico amplified DNA fragment, excluding primers.")
+ 
+    group.add_argument('--restrict-to-taxid', '-r',
+                       action="append", 
+                       dest="ecopcr:restrict-to-taxid",
+                       metavar="<TAXID>",
+                       type=int,
+                       default=[],
+                       help="Only the sequence records corresponding to the taxonomic group identified "
+                            "by TAXID are considered for the in silico PCR. The TAXID is an integer "
+                            "that can be found in the NCBI taxonomic database.")
+ 
+    group.add_argument('--ignore-taxid', '-i',
+                       action="append", 
+                       dest="ecopcr:ignore-taxid",
+                       metavar="<TAXID>",
+                       type=int,
+                       default=[],
+                       help="The sequences of the taxonomic group identified by TAXID are not considered for the in silico PCR.")
+
+    group.add_argument('--circular', '-c',
+                       action="store_true", 
+                       dest="ecopcr:circular",
+                       default=False,
+                       help="Considers that the input sequences are circular (e.g. mitochondrial or chloroplastic DNA).")
+
+    group.add_argument('--salt-concentration', '-a',
+                       action="store", 
+                       dest="ecopcr:salt-concentration",
+                       metavar="<FLOAT>",
+                       type=float,
+                       default=0.05,
+                       help="Salt concentration used for estimating the Tm. Default: 0.05.")
+
+    group.add_argument('--salt-correction-method', '-m',
+                       action="store", 
+                       dest="ecopcr:salt-correction-method",
+                       metavar="<1|2>",
+                       type=int,
+                       default=1,
+                       help="Defines the method used for estimating the Tm (melting temperature) between the primers and their corresponding "
+                            "target sequences. SANTALUCIA: 1, or OWCZARZY: 2. Default: 1.")
+
+    group.add_argument('--keep-primers', '-p',
+                       action="store_true", 
+                       dest="ecopcr:keep-primers",
+                       default=False,
+                       help="Whether to keep the primers attached to the output sequences (default: the primers are cut out).")
+
+    group.add_argument('--keep-nucs', '-D',
+                       action="store", 
+                       dest="ecopcr:keep-nucs",
+                       metavar="<N>",
+                       type=int,
+                       default=0,
+                       help="Keeps N nucleotides on each side of the in silico amplified sequences, "
+                            "not including the primers (implying that primers are automatically kept if N > 0).")
+
+    group.add_argument('--kingdom-mode', '-k',
+                       action="store_true", 
+                       dest="ecopcr:kingdom-mode",
+                       default=False,
+                       help="Print in the output the kingdom of the in silico amplified sequences (default: print the superkingdom).")
+
+ 
+
+def run(config):
+
+    cdef int32_t* restrict_to_taxids_p = NULL
+    cdef int32_t* ignore_taxids_p = NULL
+    
+    restrict_to_taxids_len = len(config['ecopcr']['restrict-to-taxid'])
+    restrict_to_taxids_p = <int32_t*> malloc((restrict_to_taxids_len + 1) * sizeof(int32_t))   # +1 for the -1 flagging the end of the array
+    for i in range(restrict_to_taxids_len) :
+        restrict_to_taxids_p[i] = config['ecopcr']['restrict-to-taxid'][i]
+    restrict_to_taxids_p[restrict_to_taxids_len] = -1
+
+    ignore_taxids_len = len(config['ecopcr']['ignore-taxid'])
+    ignore_taxids_p = <int32_t*> malloc((ignore_taxids_len + 1) * sizeof(int32_t))   # +1 for the -1 flagging the end of the array
+    for i in range(ignore_taxids_len) :
+        ignore_taxids_p[i] = config['ecopcr']['ignore-taxid'][i]
+    ignore_taxids_p[ignore_taxids_len] = -1
+    
+    DMS.obi_atexit()
+    
+    logger("info", "obi ecopcr")
+
+    # Open the input: only the DMS
+    input = open_uri(config['obi']['inputURI'],
+                     dms_only=True)
+    if input is None:
+        raise Exception("Could not read input")
+    i_dms = input[0]
+    i_dms_name = input[0].name
+    i_view_name = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output")
+    o_dms = output[0]
+    output_0 = output[0]
+    o_dms_name = output[0].name
+    o_view_name = output[1]
+
+    # Open the taxonomy DMS
+    taxdms = open_uri(config['obi']['taxoURI'],
+                     dms_only=True)
+    if taxdms is None:
+        raise Exception("Could not open taxonomy DMS")
+    tax_dms = taxdms[0]
+    tax_dms_name = taxdms[0].name
+    
+    # Read taxonomy name    
+    taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
+
+    # If stdout output create a temporary view in the input dms that will be deleted afterwards.
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+    
+    # Save command config in View comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[i_dms_name]
+    input_view_name= [i_view_name]
+    input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+    input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+
+    comments = View.print_config(config, "ecopcr", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+
+    # TODO: primers in comments?
+
+    if obi_ecopcr(i_dms.name_with_full_path, tobytes(i_view_name), 
+                  tax_dms.name_with_full_path, tobytes(taxonomy_name), \
+                  o_dms.name_with_full_path, tobytes(o_view_name), comments, \
+                  tobytes(config['ecopcr']['primer1']), tobytes(config['ecopcr']['primer2']), \
+                  config['ecopcr']['error'], \
+                  config['ecopcr']['min-length'], config['ecopcr']['max-length'], \
+                  restrict_to_taxids_p, ignore_taxids_p, \
+                  config['ecopcr']['circular'], config['ecopcr']['salt-concentration'], config['ecopcr']['salt-correction-method'], \
+                  config['ecopcr']['keep-nucs'], config['ecopcr']['keep-primers'], config['ecopcr']['kingdom-mode']) < 0:
+        raise Exception("Error running ecopcr")
+
+    # Save command config in DMS comments
+    o_dms.record_command_line(command_line)
+
+    free(restrict_to_taxids_p)
+    free(ignore_taxids_p)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_dms[o_view_name]), file=sys.stderr)
+
+    # If stdout output, delete the temporary result view in the input DMS
+    if type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+
+    i_dms.close(force=True)
+    o_dms.close(force=True)
+
+    logger("info", "Done.")

python/obitools3/commands/ecotag.pyx

@@ -0,0 +1,158 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms.dms cimport DMS
+from obitools3.dms.view import RollbackException
+from obitools3.dms.capi.obiecotag cimport obi_ecotag
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+from obitools3.dms.view.view cimport View
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+
+import sys
+from io import BufferedWriter
+
+
+__title__="Taxonomic assignment of sequences"
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+ 
+    group = parser.add_argument_group('obi ecotag specific options')
+
+    group.add_argument('--ref-database','-R',
+                      action="store", dest="ecotag:ref_view",
+                      metavar='<REF_VIEW>',
+                      type=str,
+                      help="URI of the view containing the reference database as built by the build_ref_db command.")
+
+    group.add_argument('--minimum-identity','-m',
+                      action="store", dest="ecotag:threshold",
+                      metavar='<THRESHOLD>',
+                      default=0.0,
+                      type=float,
+                      help="Minimum identity to consider for assignment, as a normalized identity, e.g. 0.95 for an identity of 95%%. "
+                           "Default: 0.00 (no threshold).")
+
+    group.add_argument('--minimum-circle','-c',
+                      action="store", dest="ecotag:bubble_threshold",
+                      metavar='<CIRCLE_THRESHOLD>',
+                      default=0.99,
+                      type=float,
+                      help="Minimum identity considered for the assignment circle "
+                           "(sequence is assigned to the LCA of all sequences within a similarity circle of the best matches; "
+                           "the threshold for this circle is the highest value between <CIRCLE_THRESHOLD> and the best assignment score found for the query sequence). "
+                           "Give value as a normalized identity, e.g. 0.95 for an identity of 95%%. "
+                           "Default: 0.99.")
+
+def run(config):
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi ecotag")
+
+    # Open the query view: only the DMS
+    input = open_uri(config['obi']['inputURI'],
+                     dms_only=True)
+    if input is None:
+        raise Exception("Could not read input")
+    i_dms = input[0]
+    i_dms_name = input[0].name
+    i_view_name = input[1]
+
+    # Open the reference view: only the DMS
+    ref = open_uri(config['ecotag']['ref_view'],
+                     dms_only=True)
+    if ref is None:
+        raise Exception("Could not read reference view URI")
+    ref_dms = ref[0]
+    ref_dms_name = ref[0].name
+    ref_view_name = ref[1]
+
+    # Check that the threshold demanded is greater than or equal to the threshold used to build the reference database
+    if config['ecotag']['bubble_threshold'] < eval(ref_dms[ref_view_name].comments["ref_db_threshold"]) :
+        raise Exception(f"Error: The threshold demanded ({config['ecotag']['bubble_threshold']}) is lower than the threshold used to build the reference database ({float(ref_dms[ref_view_name].comments['ref_db_threshold'])}).")
+    
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output")
+    o_dms = output[0]
+    output_0 = output[0]
+    final_o_view_name = output[1]
+    
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
+
+    # Read taxonomy DMS and name
+    taxo = open_uri(config['obi']['taxoURI'],
+                    dms_only=True)
+    taxo_dms_name = taxo[0].name
+    taxo_dms = taxo[0]
+    taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
+
+    # Save command config in View comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[i_dms_name]
+    input_view_name= [i_view_name]
+    input_dms_name.append(ref_dms_name)
+    input_view_name.append(ref_view_name)
+    input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+    input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    comments = View.print_config(config, "ecotag", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+
+    if obi_ecotag(i_dms.name_with_full_path, tobytes(i_view_name), \
+                  ref_dms.name_with_full_path, tobytes(ref_view_name), \
+                  taxo_dms.name_with_full_path, tobytes(taxonomy_name), \
+                  tobytes(o_view_name), comments, \
+                  config['ecotag']['threshold'], \
+                  config['ecotag']['bubble_threshold']) < 0:
+        raise Exception("Error running ecotag")
+    
+    # If the input and output DMS are not the same, export result view to output DMS
+    if i_dms != o_dms:
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+    
+    # Save command config in DMS comments
+    o_dms.record_command_line(command_line)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close(force=True)
+    
+    taxo_dms.close(force=True)
+    ref_dms.close(force=True)
+    i_dms.close(force=True)
+    
+    logger("info", "Done.")
+

python/obitools3/commands/export.pyx

@@ -0,0 +1,189 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.dms import DMS
+from obitools3.dms.obiseq import Nuc_Seq
+from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
+from obitools3.writers.tab import TabWriter
+from obitools3.format.tab import TabFormat
+from obitools3.utils cimport tobytes, tostr
+
+from obitools3.apps.optiongroups import addMinimalInputOption, \
+                                        addExportOutputOption, \
+                                        addNoProgressBarOption
+
+import sys
+import io
+
+from cpython.exc cimport PyErr_CheckSignals
+
+__title__="Export a view to a different file format"
+
+
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addExportOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+
+def run(config):
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi export : exports a view to a different file format")
+    
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input")
+    iview = input[1]
+    
+    if 'outputformat' not in config['obi']:
+        if iview.type == b"NUC_SEQS_VIEW":
+            if QUALITY_COLUMN in iview:
+                config['obi']['outputformat'] = b'fastq'
+            else:
+                config['obi']['outputformat'] = b'fasta'
+        else:
+            config['obi']['outputformat'] = b'tabular'
+    
+    # Open the output
+    output = open_uri(config['obi']['outputURI'],
+                      input=False)
+    if output is None:
+        raise Exception("Could not open output URI")
+
+    output_object = output[0]
+    writer = output[1]
+        
+     # Check that the input view has the type NUC_SEQS if needed    # TODO discuss, maybe bool property
+    if (output[2] == Nuc_Seq) and (iview.type != b"NUC_SEQS_VIEW") :  # Nuc_Seq_Stored? TODO
+        raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
+    
+    if config['obi']['only'] is not None:
+        withoutskip = min(input[4], config['obi']['only'])
+    else:
+        withoutskip = input[4]
+     
+    if config['obi']['skip'] is not None:
+        skip = min(input[4], config['obi']['skip'])
+    else:
+        skip = 0
+    
+    # Initialize the progress bar
+    if config['obi']['noprogressbar']:
+        pb = None
+    else:
+        pb = ProgressBar(withoutskip - skip, config)
+
+    if config['obi']['outputformat'] == b'metabaR':
+        # Check prefix
+        if "metabarprefix" not in config["obi"]:
+            raise Exception("Prefix needed when exporting for metabaR (--metabaR-prefix option)")
+        else:
+            metabaRprefix = config["obi"]["metabarprefix"]
+        
+    i=0
+    for seq in iview :
+        PyErr_CheckSignals()
+        if pb is not None:
+            pb(i)
+        try:
+            writer(seq)
+        except (StopIteration, BrokenPipeError, IOError):
+            break
+        i+=1
+
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+
+    if config['obi']['outputformat'] == b'metabaR':
+        
+        # Export ngsfilter file if view provided
+        if 'metabarngsfilter' in config['obi']:
+            ngsfilter_input = open_uri(config['obi']['metabarngsfilter'])
+            if ngsfilter_input is None:
+                raise Exception("Could not read ngsfilter view for metabaR output")
+            ngsfilter_view = ngsfilter_input[1]
+    
+            ngsfilter_output = open(config['obi']['metabarprefix']+'.ngsfilter', 'w')
+            
+            for line in ngsfilter_view:
+
+                line_to_print = b""                
+                line_to_print += line[b'experiment']
+                line_to_print += b"\t"
+                line_to_print += line[b'sample']
+                line_to_print += b"\t"
+                line_to_print += line[b'forward_tag']
+                line_to_print += b":"
+                line_to_print += line[b'reverse_tag']
+                line_to_print += b"\t"
+                line_to_print += line[b'forward_primer']
+                line_to_print += b"\t"
+                line_to_print += line[b'reverse_primer']
+                line_to_print += b"\t"
+                line_to_print += line[b'additional_info']
+                
+                print(tostr(line_to_print), file=ngsfilter_output)
+            
+            if ngsfilter_input[0] != input[0]:
+                ngsfilter_input[0].close()
+            ngsfilter_output.close()
+            
+        # Export sample metadata
+        samples_output = open(config['obi']['metabarprefix']+'_samples.csv', 'w')
+
+        # Export sample metadata file if view provided
+        if 'metabarsamples' in config['obi']:
+            samples_input = open_uri(config['obi']['metabarsamples'])
+            if samples_input is None:
+                raise Exception("Could not read sample view for metabaR output")
+            samples_view = samples_input[1]
+        
+            # Export with tab formatter
+            TabWriter(TabFormat(header=True, sep='\t',), 
+                      samples_output,
+                      header=True)
+            
+            if samples_input[0] != input[0]:
+                samples_input[0].close()
+        
+        # Else export just sample names from main view
+        else:
+            
+            sample_list = []
+            if 'MERGED_sample' in iview:
+                sample_list = iview['MERGED_sample'].keys()
+            elif 'sample' not in iview:
+                for seq in iview:
+                    sample = seq['sample']
+                    if sample not in sample_list:
+                        sample_list.append(sample)
+            else:
+                logger("warning", "Can not read sample list from main view for metabaR sample list export")            
+            
+            print("sample_id", file=samples_output)
+            for sample in sample_list:
+                line_to_print = b""                
+                line_to_print += sample
+                line_to_print += b"\t"
+                print(tostr(line_to_print), file=samples_output)
+        
+        samples_output.close()
+
+    # TODO save command in input dms?
+    
+    if not BrokenPipeError and not IOError:
+        output_object.close()
+    iview.close()
+    input[0].close(force=True)
+
+    logger("info", "Done.")
+
+    if BrokenPipeError or IOError:
+        sys.stderr.close()

python/obitools3/commands/grep.pyx

@@ -0,0 +1,416 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+
+from functools import reduce
+import time
+import re
+import sys
+import ast
+from io import BufferedWriter
+from cpython.exc cimport PyErr_CheckSignals
+
+ 
+__title__="Grep view lines that match the given predicates"
+
+
+# TODO should sequences that have a grepped attribute at None be grepped or not? (in obi1 they are but....)
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group("obi grep specific options")
+ 
+    group.add_argument("--predicate", "-p",
+                       action="append", dest="grep:grep_predicates",
+                       metavar="<PREDICATE>",
+                       default=[],
+                       type=str,
+                       help="Python boolean expression to be evaluated in the "
+                            "sequence/line context. The attribute name can be "
+                            "used in the expression as a variable name. "
+                            "An extra variable named 'sequence' or 'line' refers "
+                            "to the sequence or line object itself. "
+                            "Several -p options can be used on the same "
+                            "command line.")
+ 
+    group.add_argument("-S", "--sequence",
+                       action="store", dest="grep:seq_pattern",
+                       metavar="<REGULAR_PATTERN>",
+                       type=str,
+                       help="Regular expression pattern used to select "
+                            "the sequence. The pattern is case insensitive.")
+    
+    group.add_argument("-D", "--definition",
+                       action="store", dest="grep:def_pattern",
+                       metavar="<REGULAR_PATTERN>",
+                       type=str,
+                       help="Regular expression pattern used to select "
+                            "the definition of the sequence. The pattern is case insensitive.")
+    
+    group.add_argument("-I", "--identifier",
+                       action="store", dest="grep:id_pattern",
+                       metavar="<REGULAR_PATTERN>",
+                       type=str,
+                       help="Regular expression pattern used to select "
+                            "the identifier of the sequence. The pattern is case insensitive.")
+    
+    group.add_argument("--id-list",
+                       action="store", dest="grep:id_list",
+                       metavar="<FILE_NAME>",
+                       type=str,
+                       help="File containing the identifiers of the sequences to select.")
+
+    group.add_argument("-a", "--attribute",
+                       action="append", dest="grep:attribute_patterns",
+                       type=str,
+                       default=[],
+                       metavar="<ATTRIBUTE_NAME>:<REGULAR_PATTERN>",
+                       help="Regular expression pattern matched against "
+                            "the attributes of the sequence. "
+                            "The pattern is case sensitive. "
+                            "Several -a options can be used on the same "
+                            "command line.")
+    
+    group.add_argument("-A", "--has-attribute",
+                       action="append", dest="grep:attributes",
+                       type=str,
+                       default=[],
+                       metavar="<ATTRIBUTE_NAME>",
+                       help="Select records with the attribute <ATTRIBUTE_NAME> "
+                            "defined (not set to NA value). "
+                            "Several -A options can be used on the same "
+                            "command line.")
+    
+    group.add_argument("-L", "--lmax",
+                       action="store", dest="grep:lmax",
+                       metavar="<MAX_LENGTH>",
+                       type=int,
+                       help="Keep sequences shorter than MAX_LENGTH.")
+                             
+    group.add_argument("-l", "--lmin",
+                       action="store", dest="grep:lmin",
+                       metavar="<MIN_LENGTH>",
+                       type=int,
+                       help="Keep sequences longer than MIN_LENGTH.")
+    
+    group.add_argument("-v", "--invert-selection",
+                       action="store_true", dest="grep:invert_selection",
+                       default=False,
+                       help="Invert the selection.")
+
+
+    group=parser.add_argument_group("Taxonomy filtering specific options")  #TODO put somewhere else? not in grep
+ 
+    group.add_argument('--require-rank',
+                       action="append", dest="grep:required_ranks",
+                       metavar="<RANK_NAME>",
+                       type=str,
+                       default=[],
+                       help="Select sequences with a taxid that is or has "
+                            "a parent of rank <RANK_NAME>.")
+     
+    group.add_argument('-r', '--required',
+                       action="append", dest="grep:required_taxids",
+                       metavar="<TAXID>",
+                       type=int,
+                       default=[],
+                       help="Select the sequences having the ancestor of taxid <TAXID>. "
+                            "If several ancestors are specified (with \n'-r taxid1 -r taxid2'), "
+                            "the sequences having at least one of them are selected.")
+     
+    # TODO useless option equivalent to -r -v?
+    group.add_argument('-i','--ignore',
+                     action="append", dest="grep:ignored_taxids",
+                     metavar="<TAXID>",
+                     type=int,
+                     default=[],
+                     help="Ignore the sequences having the ancestor of taxid <TAXID>. "
+                          "If several ancestors are specified (with \n'-r taxid1 -r taxid2'), "
+                          "the sequences having at least one of them are ignored.")
+
+
+def obi_compile_eval(str expr):
+    
+    class MyVisitor(ast.NodeTransformer):
+        def visit_Str(self, node: ast.Str):
+            result = ast.Bytes(s = node.s.encode('utf-8'))
+            return ast.copy_location(result, node)
+   
+    expr = "obi_eval_result="+expr
+    tree = ast.parse(expr)
+    optimizer = MyVisitor()
+    tree = optimizer.visit(tree)
+    return compile(tree, filename="<ast>", mode="exec")
+
+    
+def obi_eval(compiled_expr, loc_env, line):
+
+    exec(compiled_expr, {}, loc_env)
+    obi_eval_result = loc_env["obi_eval_result"]
+    return obi_eval_result
+    
+
+def Filter_generator(options, tax_filter, i_view):
+
+    # Initialize conditions
+    predicates = None
+    if "grep_predicates" in options:
+        predicates = [obi_compile_eval(p) for p in options["grep_predicates"]]
+    attributes = None
+    if "attributes" in options and len(options["attributes"]) > 0:
+        attributes = options["attributes"]
+        for attribute in attributes:
+            if attribute not in i_view:
+                return None
+    lmax = None
+    if "lmax" in options:
+        lmax = options["lmax"]
+    lmin = None
+    if "lmin" in options:
+        lmin = options["lmin"]
+    invert_selection = options["invert_selection"]
+    id_set = None
+    if "id_list" in options:
+        id_set = set(x.strip() for x in open(options["id_list"], 'rb'))
+
+    # Initialize the regular expression patterns
+    seq_pattern = None
+    if "seq_pattern" in options:
+        seq_pattern = re.compile(tobytes(options["seq_pattern"]), re.I)
+    id_pattern = None
+    if "id_pattern" in options:
+        id_pattern = re.compile(tobytes(options["id_pattern"]))
+    def_pattern = None
+    if "def_pattern" in options:
+        def_pattern = re.compile(tobytes(options["def_pattern"]))
+    attribute_patterns={}
+    if "attribute_patterns" in options and len(options["attribute_patterns"]) > 0:
+        for p in options["attribute_patterns"]:
+            attribute, pattern = p.split(":", 1)
+            if attribute not in i_view:
+                return None
+            attribute_patterns[tobytes(attribute)] = re.compile(tobytes(pattern))
+    
+    def filter(line, loc_env):
+        cdef bint good = True
+        
+        if seq_pattern and hasattr(line, "seq"):
+            good = <bint>(seq_pattern.search(line.seq))
+        
+        if good and id_pattern and hasattr(line, "id"):
+            good = <bint>(id_pattern.search(line.id))
+            
+        if good and id_set is not None and hasattr(line, "id"):
+            good = line.id in id_set
+            
+        if good and def_pattern and hasattr(line, "definition"):
+            good = <bint>(def_pattern.search(line.definition))
+             
+        if good and attributes:  # TODO discuss that we test not None
+            good = reduce(lambda bint x, bint y: x and y,
+                           (line[attribute] is not None for attribute in attributes),
+                           True)
+             
+        if good and attribute_patterns:
+            good = (reduce(lambda bint x, bint y : x and y, 
+                        (line[attribute] is not None for attribute in attribute_patterns),
+                        True)
+                    and
+                    reduce(lambda bint x, bint y: x and y,
+                        (<bint>(attribute_patterns[attribute].search(tobytes(str(line[attribute]))))
+                        for attribute in attribute_patterns), 
+                        True)
+                   )
+                     
+        if good and predicates:
+            good = (reduce(lambda bint x, bint y: x and y,
+                    (bool(obi_eval(p, loc_env, line))
+                    for p in predicates), True))
+
+        if good and lmin:
+            good = len(line) >= lmin
+             
+        if good and lmax:
+            good = len(line) <= lmax
+         
+        if good:
+            good = tax_filter(line)
+       
+        if invert_selection :
+            good = not good
+
+        return good
+    
+    return filter
+
+
+def Taxonomy_filter_generator(taxo, options):
+    
+    if (("required_ranks" in options and options["required_ranks"]) or \
+       ("required_taxids" in options and options["required_taxids"]) or \
+       ("ignored_taxids" in options and options["ignored_taxids"])) and \
+       (taxo is None):
+        raise RollbackException("obi grep error: can't use taxonomy options without providing a taxonomy. Rollbacking view")
+    
+    if taxo is not None:
+        def tax_filter(seq):
+            good = True
+            if b'TAXID' in seq and seq[b'TAXID'] is not None:   # TODO use macro
+                taxid = seq[b'TAXID']
+                if "required_ranks" in options and options["required_ranks"]:
+                    taxon_at_rank = reduce(lambda x,y: x and y,
+                                           (taxo.get_taxon_at_rank(seq[b'TAXID'], rank) is not None
+                                            for rank in options["required_ranks"]),
+                                           True)
+                    good = good and taxon_at_rank 
+                if "required_taxids" in options and options["required_taxids"]:
+                    good = good and reduce(lambda x,y: x or y,
+                                           (taxo.is_ancestor(r, taxid) 
+                                            for r in options["required_taxids"]),
+                                           False)
+                if "ignored_taxids" in options and options["ignored_taxids"]:
+                    good = good and not reduce(lambda x,y: x or y,
+                                               (taxo.is_ancestor(r,taxid) 
+                                                for r in options["ignored_taxids"]),
+                                               False)
+            return good
+    else:
+        def tax_filter(seq):
+            return True
+    return tax_filter
+
+
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi grep")
+
+    # Open the input
+    input = open_uri(config["obi"]["inputURI"])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    final_o_view_name = output[1]
+
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted afterwards.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
+
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        taxo_uri = open_uri(config["obi"]["taxoURI"])
+        if taxo_uri is None or taxo_uri[2] == bytes:
+            raise Exception("Couldn't open taxonomy")
+        taxo = taxo_uri[1]
+    else :
+        taxo = None
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(i_view), config)
+    else:
+        pb = None
+ 
+    # Apply filter
+    tax_filter = Taxonomy_filter_generator(taxo, config["grep"])
+    filter = Filter_generator(config["grep"], tax_filter, i_view)        
+    selection = Line_selection(i_view)
+    
+    if filter is None and config["grep"]["invert_selection"]: # all sequences are selected: filter is None if no line will be selected because some columns don't exist
+        for i in range(len(i_view)):
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            selection.append(i)
+    
+    elif filter is not None :   # filter is None if no line will be selected because some columns don't exist
+        for i in range(len(i_view)):
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            line = i_view[i]
+            
+            loc_env = {"sequence": line, "line": line, "taxonomy": taxo, "obi_eval_result": False}
+            
+            good = filter(line, loc_env)
+     
+            if good :
+                selection.append(i)
+   
+    if pb is not None:
+        pb(len(i_view), force=True)
+        print("", file=sys.stderr)
+
+    # Create output view with the line selection
+    try:
+        o_view = selection.materialize(o_view_name)
+    except Exception, e:
+        raise RollbackException("obi grep error, rollbacking view: "+str(e), o_view)
+
+    logger("info", "Grepped %d entries" % len(o_view))
+
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[input[0].name]
+    input_view_name=[input[1].name]
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+        input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    o_view.write_config(config, "grep", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
+
+    # If input and output DMS are not the same, export the temporary view to the output DMS
+    # and delete the temporary view in the input DMS
+    if i_dms != o_dms:
+        o_view.close()
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+        o_view = o_dms[final_o_view_name]
+    
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close(force=True)
+    i_dms.close(force=True)
+
+    logger("info", "Done.")

python/obitools3/commands/head.pyx

@@ -0,0 +1,129 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
+from obitools3.apps.optiongroups import addExportOutputOption
+
+import time
+import sys
+from io import BufferedWriter
+
+from cpython.exc cimport PyErr_CheckSignals
+
+
+__title__="Keep the N first lines of a view"
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+    addExportOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi head specific options')
+
+    group.add_argument('-n', '--sequence-count',
+                       action="store", dest="head:count",
+                       metavar='<N>',
+                       default=10,
+                       type=int,
+                       help="Number of first records to keep.")
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi head")
+
+    # Open the input
+    input = open_uri(config["obi"]["inputURI"])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    final_o_view_name = output[1]
+    
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
+    
+    n = min(config['head']['count'], len(i_view))
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(n, config)
+    else:
+        pb = None
+        
+    selection = Line_selection(i_view)
+    
+    for i in range(n):
+        PyErr_CheckSignals()
+        if pb is not None:
+            pb(i)
+        selection.append(i)
+
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+
+    # Create output view with the line selection
+    try:
+        o_view = selection.materialize(o_view_name)
+    except Exception, e:
+        raise RollbackException("obi head error, rollbacking view: "+str(e), o_view)
+    
+    # Save command config in DMS comments
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "head", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
+    o_dms.record_command_line(command_line)
+
+    # If input and output DMS are not the same, export the temporary view to the output DMS
+    # and delete the temporary view in the input DMS
+    if i_dms != o_dms:
+        o_view.close()
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+        o_view = o_dms[final_o_view_name]
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(view), file=sys.stderr)
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close(force=True)
+    i_dms.close(force=True)
+    
+    logger("info", "Done.")

python/obitools3/commands/history.pyx

@@ -0,0 +1,58 @@
+#cython: language_level=3
+
+from obitools3.apps.optiongroups import addMinimalInputOption
+from obitools3.uri.decode import open_uri
+from obitools3.dms import DMS
+from obitools3.dms.view import View
+from obitools3.utils cimport bytes2str
+
+ 
+__title__="Command line histories and view history graphs"
+ 
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+ 
+    group=parser.add_argument_group('obi history specific options')
+ 
+    group.add_argument('--bash', '-b',
+                     action="store_const", dest="history:format",
+                     default="bash",
+                     const="bash",
+                     help="Print history in bash format")
+
+    group.add_argument('--dot', '-d',
+                     action="store_const", dest="history:format",
+                     default="bash",
+                     const="dot",
+                     help="Print history in DOT format (default: bash format)")
+
+    group.add_argument('--ascii', '-a',
+                     action="store_const", dest="history:format",
+                     default="bash",
+                     const="ascii",
+                     help="Print history in ASCII format (only for views; default: bash format)")
+ 
+
+def run(config):
+    
+    cdef object entries
+    
+    DMS.obi_atexit()
+    
+    input = open_uri(config['obi']['inputURI'])
+       
+    entries = input[1]
+    
+    if config['history']['format'] == "bash" :
+        print(bytes2str(entries.bash_history))
+    elif config['history']['format'] == "dot" :
+        print(bytes2str(entries.dot_history_graph))
+    elif config['history']['format'] == "ascii" :
+        if isinstance(entries, View):
+            print(bytes2str(entries.ascii_history))
+        else:
+            raise Exception("ASCII history only available for views")
+    
+    input[0].close(force=True)

python/obitools3/commands/import.pyx

@@ -0,0 +1,552 @@
+#cython: language_level=3
+
+import sys
+import os
+import re
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms.view.view cimport View
+from obitools3.dms.view import RollbackException
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+from obitools3.dms.column.column cimport Column
+from obitools3.dms.obiseq cimport Nuc_Seq
+from obitools3.dms import DMS
+from obitools3.dms.taxo.taxo cimport Taxonomy
+from obitools3.files.uncompress cimport CompressedFile
+
+
+from obitools3.utils cimport tobytes, \
+                             tostr, \
+                             get_obitype, \
+                             update_obitype
+
+from obitools3.dms.capi.obiview cimport VIEW_TYPE_NUC_SEQS, \
+                                        NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN, \
+                                        MERGED_PREFIX, \
+                                        SCIENTIFIC_NAME_COLUMN
+                                        
+from obitools3.dms.capi.obidms cimport obi_import_view
+
+from obitools3.dms.capi.obitypes cimport obitype_t, \
+                                         OBI_VOID, \
+                                         OBI_QUAL, \
+                                         OBI_STR, \
+                                         OBI_INT
+
+from obitools3.dms.capi.obierrno cimport obi_errno
+
+from obitools3.apps.optiongroups import addImportInputOption, \
+                                        addTabularInputOption, \
+                                        addTaxdumpInputOption, \
+                                        addMinimalOutputOption, \
+                                        addNoProgressBarOption, \
+                                        addTaxonomyOption
+
+from obitools3.uri.decode import open_uri
+
+from obitools3.apps.config import logger
+
+from cpython.exc cimport PyErr_CheckSignals
+
+from io import BufferedWriter
+import ast
+
+
+__title__="Import sequences from different formats into a DMS"
+ 
+ 
+default_config = {   'destview'     : None,
+                     'skip'         : 0,
+                     'only'         : None,
+                     'skiperror'    : False,
+                     'seqinformat'  : None,
+                     'moltype'      : 'nuc',
+                     'source'     : None
+                 }
+
+def addOptions(parser):
+    
+    addImportInputOption(parser)
+    addTabularInputOption(parser)
+    addTaxdumpInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group = parser.add_argument_group('obi import specific options')
+
+    group.add_argument('--preread',
+                     action="store_true", dest="import:preread",
+                     default=False,
+                     help="Do a first readthrough of the dataset if it contains huge dictionaries (more than 100 keys) for "
+                          "a much faster import. This option is not recommended and will slow down the import in any other case.")
+
+    group.add_argument('--space-priority',
+                     action="store_true", dest="import:space_priority",
+                     default=False,
+                     help="If importing a view into another DMS, do it by importing each line, saving disk space if the original view "
+                          "has a line selection associated.")
+
+#    group.add_argument('--only-id',
+#                     action="store", dest="import:onlyid",
+#                     help="only id")
+
+def run(config):
+    
+    cdef   tuple       input
+    cdef   tuple       output 
+    cdef   int         i
+    cdef   type        value_type
+    cdef   obitype_t   value_obitype
+    cdef   obitype_t   old_type
+    cdef   obitype_t   new_type
+    cdef   bint        get_quality
+    cdef   bint        NUC_SEQS_view
+    cdef   bint        silva
+    cdef   bint        rdp
+    cdef   bint        unite
+    cdef   bint        sintax
+    cdef   int         nb_elts
+    cdef   object      d
+    cdef   View        view
+    cdef   object      entries
+    cdef   object      entry
+    cdef   Column      id_col
+    cdef   Column      def_col
+    cdef   Column      seq_col
+    cdef   Column      qual_col
+    cdef   Column      old_column
+    cdef   Column      sci_name_col
+    cdef   bytes       sci_name
+    cdef   bint        rewrite
+    cdef   dict        dcols
+    cdef   int         skipping
+    cdef   bytes       tag
+    cdef   object      value
+    cdef   list        elt_names
+    cdef   int         old_nb_elements_per_line
+    cdef   int         new_nb_elements_per_line
+    cdef   list        old_elements_names
+    cdef   list        new_elements_names
+    cdef   ProgressBar pb
+    global             obi_errno
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi import: imports an object (file(s), obiview, taxonomy...) into a DMS")
+    
+    entry_count = -1
+    pb = None
+    
+    if not config['obi']['taxdump']:
+        input = open_uri(config['obi']['inputURI'])
+        if input is None:  # TODO check for bytes instead now?
+            raise Exception("Could not open input URI")
+        
+        if config['obi']['only'] is not None:
+            entry_count = min(input[4], config['obi']['only'])
+        else:
+            entry_count = input[4]
+        
+        if entry_count > 0:
+            logger("info", "Importing %d entries", entry_count)
+        else:
+            logger("info", "Importing an unknown number of entries")
+        
+        # TODO a bit dirty?
+        if input[2]==Nuc_Seq or input[2]==View_NUC_SEQS:
+            v = View_NUC_SEQS
+        else:
+            v = View 
+    else:
+        v = None
+    
+    if config['obi']['taxdump'] or (isinstance(input[1], View) and not config['import']['space_priority']): 
+        dms_only=True
+    else:
+        dms_only=False
+    
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      newviewtype=v,
+                      dms_only=dms_only)
+    if output is None:
+        raise Exception("Could not open output")
+    
+    o_dms = output[0]
+    
+    # Read taxdump
+    if config['obi']['taxdump']:  # The input is a taxdump to import in a DMS
+        # Check if taxonomy name isn't already taken
+        taxo_name = output[1].split(b'/')[1]
+        if Taxonomy.exists(o_dms, taxo_name):
+            raise Exception("Taxonomy name already exists in this DMS")
+        taxo = Taxonomy.open_taxdump(o_dms, config['obi']['inputURI'])
+        taxo.write(taxo_name)
+        taxo.close()
+        o_dms.record_command_line(" ".join(sys.argv[1:]))
+        o_dms.close(force=True)
+        logger("info", "Done.")
+        return
+
+    # Open taxonomy if there is one
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        taxo_uri = open_uri(config['obi']['taxoURI'])
+        if taxo_uri is None or taxo_uri[2] == bytes:
+            raise Exception("Couldn't open taxonomy")
+        taxo = taxo_uri[1]
+
+    else :
+        taxo = None
+
+    # If importing a view between two DMS and not wanting to save space if line selection in original view, use C API
+    if isinstance(input[1], View) and not config['import']['space_priority']:
+        if obi_import_view(input[0].name_with_full_path, o_dms.name_with_full_path, input[1].name, tobytes((config['obi']['outputURI'].split('/'))[-1])) < 0 :
+            input[0].close(force=True)
+            output[0].close(force=True)
+            raise Exception("Error importing a view in a DMS")
+        o_dms.record_command_line(" ".join(sys.argv[1:]))
+        input[0].close(force=True)
+        output[0].close(force=True)
+        logger("info", "Done.")
+        return
+
+    # Reinitialize the progress bar
+    if entry_count >= 0 and config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(entry_count, config)
+    else:
+        pb = None
+        
+    NUC_SEQS_view = False
+    if isinstance(output[1], View) :
+        view = output[1]
+        if output[2] == View_NUC_SEQS :
+            NUC_SEQS_view = True
+    else: 
+        raise NotImplementedError()
+
+    # Save basic columns in variables for optimization
+    if NUC_SEQS_view :
+        id_col = view[ID_COLUMN]
+        def_col = view[DEFINITION_COLUMN]
+        seq_col = view[NUC_SEQUENCE_COLUMN]
+
+    # Prepare taxon scientific name and taxid refs if RDP/SILVA/UNITE/SINTAX formats
+    silva = False
+    rdp = False
+    unite = False
+    sintax=False
+    if 'inputformat' in config['obi'] and (config['obi']['inputformat'] == b"silva" or \
+                                           config['obi']['inputformat'] == b"rdp" or \
+                                           config['obi']['inputformat'] == b"unite" or \
+                                           config['obi']['inputformat'] == b"sintax"):
+        #if taxo is None:
+        #    raise Exception("A taxonomy (as built by 'obi import --taxdump') must be provided for SILVA and RDP files")
+        if config['obi']['inputformat'] == b"silva":
+            silva = True
+        elif config['obi']['inputformat'] == b"rdp":
+            rdp = True
+        elif config['obi']['inputformat'] == b"unite":
+            unite = True
+        elif config['obi']['inputformat'] == b"sintax":
+            sintax = True
+        sci_name_col = Column.new_column(view, SCIENTIFIC_NAME_COLUMN, OBI_STR)
+        if taxo is not None:
+            taxid_col = Column.new_column(view, TAXID_COLUMN, OBI_INT)
+
+    dcols = {}
+
+    # First read through the entries to prepare columns with dictionaries as they are very time-expensive to rewrite
+    if config['import']['preread']:
+        logger("info", "First readthrough...")
+        entries = input[1]
+        i = 0
+        dict_dict = {}
+        for entry in entries:
+            PyErr_CheckSignals()
+        
+            if entry is None:  # error or exception handled at lower level, not raised because Python generators can't resume after any exception is raised
+                if config['obi']['skiperror']:
+                    i-=1
+                    continue
+                else:
+                    raise Exception("obi import error in first readthrough")
+            
+            if pb is not None:
+                pb(i)
+            elif not i%50000:
+                logger("info", "Read %d entries", i)
+    
+            for tag in entry :
+                newtag = tag
+                if tag[:7] == b"merged_":
+                    newtag = MERGED_PREFIX+tag[7:]
+                if type(entry[tag]) == dict :
+                    if tag in dict_dict:
+                        dict_dict[newtag][0].update(entry[tag].keys())
+                    else:
+                        dict_dict[newtag] = [set(entry[tag].keys()), get_obitype(entry[tag])]
+            i+=1
+        
+        if pb is not None:
+            pb(i, force=True)
+            print("", file=sys.stderr)
+       
+        for tag in dict_dict:
+            dcols[tag] = (Column.new_column(view, tag, dict_dict[tag][1], \
+                              nb_elements_per_line=len(dict_dict[tag][0]), \
+                              elements_names=list(dict_dict[tag][0]), \
+                              dict_column=True), \
+                          dict_dict[tag][1])
+    
+        
+        # Reinitialize the input
+        if isinstance(input[0], CompressedFile):
+            input_is_file = True
+        
+        # Reinitialize the progress bar
+        if entry_count >= 0 and config['obi']['noprogressbar'] == False:
+            pb = ProgressBar(entry_count, config)
+        else:
+            pb = None
+
+        try:
+            input[0].close()
+        except AttributeError:
+            pass
+        input = open_uri(config['obi']['inputURI'], force_file=input_is_file)
+        if input is None:
+            raise Exception("Could not open input URI")
+    
+#    if 'onlyid' in config['import']:
+#        onlyid = tobytes(config['import']['onlyid'])
+#    else:
+#        onlyid = None
+    
+    entries = input[1]
+    i = 0
+    for entry in entries :
+        
+        PyErr_CheckSignals()
+
+        if entry is None:  # error or exception handled at lower level, not raised because Python generators can't resume after any exception is raised
+            if config['obi']['skiperror']:
+                continue
+            else:
+                raise RollbackException("obi import error, rollbacking view", view)
+        
+        if pb is not None:
+            pb(i)
+        elif not i%50000:
+            logger("info", "Imported %d entries", i)
+        
+#        if onlyid is not None and entry.id != onlyid:
+#            continue
+        
+        try:
+             
+            if NUC_SEQS_view: 
+                id_col[i] = entry.id           
+                def_col[i] = entry.definition
+                seq_col[i] = entry.seq
+                # Check if there is a sequencing quality associated by checking the first entry    # TODO haven't found a more robust solution yet
+                if i == 0:
+                    get_quality = QUALITY_COLUMN in entry
+                    if get_quality:
+                        Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)
+                        qual_col = view[QUALITY_COLUMN]
+                if get_quality:
+                    qual_col[i] = entry.quality
+                    
+                # Parse taxon scientific name if RDP or Silva or Unite file
+                if (rdp or silva or unite or sintax):
+                    if rdp or silva:
+                        sci_names = entry.definition.split(b";")
+                        sci_name_col[i] = sci_names[-1]
+                    elif unite:
+                        sci_names = entry.id.split(b'|')[-1].split(b';')
+                        sci_name_col[i] = re.sub(b'[a-zA-Z]__', b'', sci_names[-1])
+                    elif sintax:
+                        reconstructed_line = entry.id+b' '+entry.definition[:-1]
+                        splitted_reconstructed_line = reconstructed_line.split(b';')
+                        taxa = splitted_reconstructed_line[1].split(b'=')[1]
+                        taxa = splitted_reconstructed_line[1].split(b',')
+                        sci_names = []
+                        for t in taxa:
+                            tf = t.split(b':')[1]
+                            sci_names.append(tf)
+                        sci_name_col[i] = sci_names[-1]
+                        id_col[i] = reconstructed_line.split(b';')[0]    
+                        def_col[i] = reconstructed_line
+                        
+                    # Fond taxid if taxonomy provided
+                    if taxo is not None :
+                        for sci_name in reversed(sci_names):
+                            if unite:
+                                sci_name = re.sub(b'[a-zA-Z]__', b'', sci_name)
+                            if sci_name.split()[0] != b'unidentified' and sci_name.split()[0] != b'uncultured' and sci_name.split()[0] != b'metagenome':
+                                taxon = taxo.get_taxon_by_name(sci_name)
+                                if taxon is not None:
+                                    sci_name_col[i] = taxon.name
+                                    taxid_col[i] = taxon.taxid
+                                    #print(taxid_col[i], sci_name_col[i])
+                                    break
+
+            for tag in entry :
+                
+                if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN :  # TODO dirty 
+                
+                    value = entry[tag]
+                    if tag == b"taxid":
+                        tag = TAXID_COLUMN
+                    if tag == b"count":
+                        tag = COUNT_COLUMN
+                    if tag == b"scientific_name":
+                        tag = SCIENTIFIC_NAME_COLUMN
+                    if tag[:7] == b"merged_":
+                        tag = MERGED_PREFIX+tag[7:]
+
+                    if type(value) == bytes and value[:1]==b"[" :
+                        try:
+                            if type(eval(value)) == list:
+                                value = eval(value)
+                                #print(value)
+                        except:
+                            pass
+                    
+                    if tag not in dcols :
+                    
+                        value_type = type(value)
+                        nb_elts = 1
+                        value_obitype = OBI_VOID
+                        dict_col = False
+                        
+                        if value_type == dict :
+                            nb_elts = len(value)
+                            elt_names = list(value)
+                            dict_col = True
+                        else :
+                            nb_elts = 1
+                            elt_names = None
+                        
+                        if value_type == list :
+                            tuples = True
+                        else:
+                            tuples = False
+                        
+                        value_obitype = get_obitype(value)
+                                                
+                        if value_obitype != OBI_VOID :
+                            dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names, dict_column=dict_col, tuples=tuples), value_obitype)
+                                                     
+                            # Fill value
+                            dcols[tag][0][i] = value
+                         
+                        # TODO else log error?
+     
+                    else :
+             
+                        rewrite = False
+     
+                        # Check type adequation
+                        old_type = dcols[tag][1]
+                        new_type = OBI_VOID
+                        new_type = update_obitype(old_type, value)
+                        if old_type != new_type :
+                            rewrite = True
+     
+                        try:
+                            # Check that it's not the case where the first entry contained a dict of length 1 and now there is a new key                        
+                            if type(value) == dict and \
+                                dcols[tag][0].nb_elements_per_line == 1 \
+                                and set(dcols[tag][0].elements_names) != set(value.keys()) :
+                                raise IndexError  # trigger column rewrite
+                            
+                            # Fill value
+                            dcols[tag][0][i] = value
+                         
+                        except (IndexError, OverflowError):
+                                                                                 
+                            value_type = type(value)
+                            old_column = dcols[tag][0]
+                            old_nb_elements_per_line = old_column.nb_elements_per_line
+                            new_nb_elements_per_line = 0
+                            old_elements_names = old_column.elements_names
+                            new_elements_names = None
+         
+                            #####################################################################
+                             
+                            # Check the length and keys of column lines if needed
+                            if value_type == dict :    # Check dictionary keys
+                                for k in value :
+                                    if k not in old_elements_names :
+                                        new_elements_names = list(set(old_elements_names+[tobytes(k) for k in value]))
+                                        rewrite = True
+                                        break
+                             
+                            elif value_type == list or value_type == tuple :  # Check vector length
+                                if old_nb_elements_per_line < len(value) :
+                                    new_nb_elements_per_line = len(value)
+                                    rewrite = True
+                             
+                            #####################################################################
+                             
+                            if rewrite :
+                                if new_nb_elements_per_line == 0 and new_elements_names is not None :
+                                    new_nb_elements_per_line = len(new_elements_names)
+                                 
+                                # Reset obierrno 
+                                obi_errno = 0
+     
+                                dcols[tag] = (view.rewrite_column_with_diff_attributes(old_column.name, 
+                                                                                       new_data_type=new_type, 
+                                                                                       new_nb_elements_per_line=new_nb_elements_per_line,
+                                                                                       new_elements_names=new_elements_names,
+                                                                                       rewrite_last_line=False), 
+                                              new_type)
+                                 
+                                # Update the dictionary:
+                                for t in dcols :
+                                    dcols[t] = (view[t], dcols[t][1])
+                                 
+                                # Fill value
+                                dcols[tag][0][i] = value
+        
+        except Exception as e:
+            print("\nCould not import sequence:\n", repr(entry), "\nError raised:", e, "\n/!\ Check if '--input-na-string' option needs to be set")
+            if 'skiperror' in config['obi'] and not config['obi']['skiperror']:
+                raise e
+            else:
+                pass
+                i-=1  # overwrite problematic entry
+        
+        i+=1
+ 
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+    logger("info", "Imported %d entries", len(view))
+    
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    view.write_config(config, "import", command_line, input_str=[os.path.abspath(config['obi']['inputURI'])])
+    output[0].record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(view), file=sys.stderr)
+    
+    try:
+        input[0].close()
+    except AttributeError:
+        pass
+    try:
+        output[0].close(force=True)
+    except AttributeError:
+        pass
+
+    logger("info", "Done.")

python/obitools3/commands/less.pyx

@@ -0,0 +1,50 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.uri.decode import open_uri
+from obitools3.dms import DMS
+from obitools3.utils cimport tobytes
+from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
+from obitools3.apps.optiongroups import addMinimalInputOption
+
+import sys
+import io
+from subprocess import Popen, PIPE
+
+from cpython.exc cimport PyErr_CheckSignals
+
+__title__="Less equivalent"
+
+
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+
+
+def run(config):
+        
+    DMS.obi_atexit()
+        
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input")
+    iview = input[1]
+    
+    process = Popen(["less"], stdin=PIPE)
+    
+    for seq in iview :
+        PyErr_CheckSignals()
+        try:
+            process.stdin.write(tobytes(repr(seq)))
+            process.stdin.write(b"\n")
+        except (StopIteration, BrokenPipeError, IOError):
+            break
+
+    sys.stderr.close()
+    process.stdin.close()
+    process.wait()
+
+    iview.close()
+    input[0].close(force=True)
+

python/obitools3/commands/ls.pyx

@@ -0,0 +1,41 @@
+#cython: language_level=3
+
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.dms import DMS
+from obitools3.dms.taxo.taxo cimport Taxonomy
+from obitools3.apps.optiongroups import addMinimalInputOption
+from obitools3.utils cimport tostr, bytes2str_object
+
+ 
+__title__="Print a preview of a DMS, view, column...."
+
+
+def addOptions(parser):    
+    addMinimalInputOption(parser)
+    group = parser.add_argument_group('obi ls specific options')
+
+    group.add_argument('-l',
+                     action="store_true", dest="ls:longformat",
+                     default=False,
+                     help="Detailed list in long format with all metadata.")
+
+
+def run(config):
+
+    DMS.obi_atexit()
+    
+    logger("info", "obi ls")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input")
+    
+    # Print representation
+    if config['ls']['longformat']:
+        print(input[1].repr_longformat())
+    else:
+        print(repr(input[1]))
+    
+    input[0].close(force=True)

python/obitools3/commands/ngsfilter.pyx

@@ -0,0 +1,720 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view import RollbackException, View
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+from obitools3.dms.column.column cimport Column, Column_line
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.libalign._freeendgapfm import FreeEndGapFullMatch
+from obitools3.libalign.apat_pattern import Primer_search
+from obitools3.dms.obiseq cimport Nuc_Seq
+from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
+from obitools3.dms.capi.apat cimport MAX_PATTERN
+from obitools3.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
+from obitools3.utils cimport tobytes, str2bytes
+
+from libc.stdint cimport INT32_MAX
+from functools import reduce
+import math
+import sys
+from cpython.exc cimport PyErr_CheckSignals
+from io import BufferedWriter
+
+
+MAX_PAT_LEN = 31
+
+
+__title__="Assign sequence records to the corresponding experiment/sample based on DNA tags and primers"
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+    
+    group = parser.add_argument_group('obi ngsfilter specific options')
+
+    group.add_argument('-t','--info-view',
+                     action="store", dest="ngsfilter:info_view",
+                     metavar="<URI>",
+                     type=str,
+                     default=None,
+                     required=True,
+                     help="URI to the view containing the samples definition (with tags, primers, sample names,...).\n"
+                          "\nWarning: primer lengths must be less than or equal to 32")
+
+    group.add_argument('-R', '--reverse-reads',
+                     action="store", dest="ngsfilter:reverse",
+                     metavar="<URI>",
+                     default=None,
+                     type=str,
+                     help="URI to the reverse reads if the paired-end reads haven't been aligned yet")
+
+    group.add_argument('-u','--unidentified',
+                     action="store", dest="ngsfilter:unidentified",
+                     metavar="<URI>",
+                     type=str,
+                     default=None,
+                     help="URI to the view used to store the sequences unassigned to any sample. Those sequences are untrimmed.")
+
+    group.add_argument('--no-tags',
+                     action="store_true", dest="ngsfilter:notags",
+                     default=False,
+                     help="Use this option if your experiment does not use tags to identify samples")
+    
+    group.add_argument('-e','--error',
+                     action="store", dest="ngsfilter:error",
+                     metavar="###",
+                     type=int,
+                     default=2,
+                     help="Number of errors allowed for matching primers [default = 2]")
+
+
+class Primer:
+    
+    collection={}
+    
+    def __init__(self, sequence, taglength, forward=True, max_errors=2, verbose=False, primer_pair_idx=0, primer_idx=0):
+        '''
+            
+        @param sequence:
+        @type sequence:
+        @param direct:
+        @type direct:
+        '''
+        
+        assert len(sequence) <= MAX_PAT_LEN, "Primer %s is too long, 31 bp max" % sequence
+        
+        assert sequence not in Primer.collection        \
+            or Primer.collection[sequence]==taglength,  \
+            "Primer %s must always be used with tags of the same length" % sequence
+            
+        Primer.collection[sequence]=taglength
+        
+        self.primer_pair_idx = primer_pair_idx
+        self.primer_idx = primer_idx
+        self.is_revcomp = False
+        self.revcomp = None
+        self.raw=sequence
+        self.sequence = Nuc_Seq(b"primer", sequence)        
+        self.lseq = len(self.sequence)
+        self.max_errors=max_errors
+        self.taglength=taglength
+        self.forward = forward
+        self.verbose=verbose
+        
+    def reverse_complement(self):
+        p = Primer(self.raw,
+                   self.taglength,
+                   not self.forward,
+                   verbose=self.verbose,
+                   max_errors=self.max_errors,
+                   primer_pair_idx=self.primer_pair_idx,
+                   primer_idx=self.primer_idx)
+        p.sequence=p.sequence.reverse_complement
+        p.is_revcomp = True
+        p.revcomp = None
+        return p
+    
+    def __hash__(self):
+        return hash(str(self.raw))
+    
+    def __eq__(self,primer):
+        return self.raw==primer.raw 
+    
+    def __call__(self, sequence, same_sequence=False, pattern=0, begin=0):
+        
+        if len(sequence) <= self.lseq:
+            return None
+                
+        ali = self.aligner.search_one_primer(sequence.seq, 
+                                             self.primer_pair_idx, 
+                                             self.primer_idx, 
+                                             reverse_comp=self.is_revcomp, 
+                                             same_sequence=same_sequence,
+                                             pattern_ref=pattern,
+                                             begin=begin)
+        
+        if ali is None:  # no match
+            return None 
+            
+        errors, start = ali.first_encountered()
+                
+        if errors <= self.max_errors:
+            end = start + self.lseq
+            if self.taglength is not None:
+                if self.sequence.is_revcomp:
+                    if (len(sequence)-end) >= self.taglength:
+                        tag_start = len(sequence) - end - self.taglength
+                        tag = sequence.reverse_complement[tag_start:tag_start+self.taglength].seq
+                    else:
+                        tag=None
+                else:
+                    if start >= self.taglength:
+                        tag = tobytes((sequence[start - self.taglength:start].seq).lower())  # turn back to lowercase because apat turned to uppercase
+                    else:
+                        tag=None
+            else:
+                tag=None
+            
+            return errors,start,end,tag
+
+        return None 
+    
+    
+    def __str__(self):
+        return "%s: %s" % ({True:'D',False:'R'}[self.forward],self.raw)
+    
+    __repr__=__str__
+
+
+cdef read_info_view(info_view, max_errors=2, verbose=False, not_aligned=False):
+    infos = {}
+    primer_list = []
+    i=0
+    for p in info_view:
+        
+        # Check primer length: should not be longer than 32, the max allowed by the apat lib
+        if len(p[b'forward_primer']) > 32:
+            raise RollbackException("Error: primers can not be longer than 32bp, rollbacking views")
+        if len(p[b'reverse_primer']) > 32:
+            raise RollbackException("Error: primers can not be longer than 32bp, rollbacking views")
+        
+        forward=Primer(p[b'forward_primer'],
+                       len(p[b'forward_tag']) if (b'forward_tag' in p and p[b'forward_tag']!=None) else None,
+                       True,
+                       max_errors=max_errors,
+                       verbose=verbose,
+                       primer_pair_idx=i,
+                       primer_idx=0)
+        
+        fp = infos.get(forward,{})
+        infos[forward]=fp
+        
+        reverse=Primer(p[b'reverse_primer'],
+                       len(p[b'reverse_tag']) if (b'reverse_tag' in p and p[b'reverse_tag']!=None) else None,
+                       False,
+                       max_errors=max_errors,
+                       verbose=verbose,
+                       primer_pair_idx=i,
+                       primer_idx=1)
+
+        primer_list.append((p[b'forward_primer'], p[b'reverse_primer']))
+        
+        rp = infos.get(reverse,{})
+        infos[reverse]=rp
+        
+        if not_aligned:
+            cf=forward
+            cr=reverse
+            
+            cf.revcomp = forward.reverse_complement()
+            cr.revcomp = reverse.reverse_complement()
+
+            dpp=fp.get(cr,{})
+            fp[cr]=dpp
+            
+            rpp=rp.get(cf,{})
+            rp[cf]=rpp
+        
+        else:
+            cf=forward.reverse_complement()
+            cr=reverse.reverse_complement()
+            
+            dpp=fp.get(cr,{})
+            fp[cr]=dpp
+             
+            rpp=rp.get(cf,{})
+            rp[cf]=rpp
+
+        tags = (p[b'forward_tag'] if (b'forward_tag' in p and p[b'forward_tag']!=None) else None,
+                p[b'reverse_tag'] if (b'reverse_tag' in p and p[b'reverse_tag']!=None) else None)
+        
+        if tags != (None, None):
+            assert tags not in dpp, \
+               "Tag pair %s is already used with primer pairs: (%s,%s)" % (str(tags),forward,reverse)
+        
+        # Save additional data
+        special_keys = [b'forward_primer', b'reverse_primer', b'forward_tag', b'reverse_tag']
+        data={}
+        for key in p:
+            if key not in special_keys:
+                data[key] = p[key]
+                            
+        dpp[tags] = data
+        rpp[tags] = data
+        
+        i+=1
+        
+    return infos, primer_list
+    
+
+cdef tuple annotate(sequences, infos, no_tags, verbose=False):
+        
+    def sortMatch(match):
+        if match[1] is None:
+            return INT32_MAX
+        else:
+            return match[1][1]
+
+    def sortReverseMatch(match):
+        if match[1] is None:
+            return -1
+        else:
+            return match[1][1]
+    
+    not_aligned = len(sequences) > 1
+    sequences[0] = sequences[0].clone()
+    
+    if not_aligned:
+        sequences[0][b"R1_parent"] = sequences[0].id
+        sequences[0][b"R2_parent"] = sequences[1].id
+
+    if not_aligned:
+        sequences[1] = sequences[1].clone()
+        sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq        # used by alignpairedend tool
+        sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality     # used by alignpairedend tool
+
+    for seq in sequences:
+        if hasattr(seq, "quality_array") and seq.quality_array is not None: 
+            q = -reduce(lambda x,y:x+y,(math.log10(z) for z in seq.quality_array),0)/len(seq.quality_array)*10
+            seq[b'avg_quality']=q
+            q = -reduce(lambda x,y:x+y,(math.log10(z) for z in seq.quality_array[0:10]),0)
+            seq[b'head_quality']=q
+            if len(seq.quality_array[10:-10]) :
+                q = -reduce(lambda x,y:x+y,(math.log10(z) for z in seq.quality_array[10:-10]),0)/len(seq.quality_array[10:-10])*10
+                seq[b'mid_quality']=q
+            q = -reduce(lambda x,y:x+y,(math.log10(z) for z in seq.quality_array[-10:]),0)
+            seq[b'tail_quality']=q
+    
+    # Try direct matching:
+    directmatch = []
+    for seq in sequences:
+        new_seq = True
+        pattern = 0
+        for p in infos:
+            if pattern == MAX_PATTERN:
+                new_seq = True
+                pattern = 0
+            # Saving original primer as 4th member of the tuple to serve as correct key in infos dict even if it might be reversed complemented (not here)
+            directmatch.append((p, p(seq, same_sequence=not new_seq, pattern=pattern), seq, p))
+            new_seq = False
+            pattern+=1
+        
+    # Choose match closer to the start of (one of the) sequence(s)
+    directmatch = sorted(directmatch, key=sortMatch)
+    all_direct_matches = directmatch
+    directmatch = directmatch[0] if directmatch[0][1] is not None else None
+
+    if directmatch is None:
+        if not_aligned:
+            sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq             # used by alignpairedend tool
+            sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality     # used by alignpairedend tool
+        sequences[0][b'error']=b'No primer match'
+        return False, sequences[0]
+
+    if id(directmatch[2]) == id(sequences[0]):
+        first_match_first_seq = True
+    else:
+        first_match_first_seq = False
+       
+    match = directmatch[2][directmatch[1][1]:directmatch[1][2]]
+    
+    if not not_aligned:
+        sequences[0][b'seq_length_ori']=len(sequences[0])
+    
+    if not not_aligned or first_match_first_seq:
+        sequences[0] = sequences[0][directmatch[1][2]:]
+    else:
+        sequences[1] = sequences[1][directmatch[1][2]:]
+        sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq      # used by alignpairedend tool
+        sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality   # used by alignpairedend tool
+    
+    if directmatch[0].forward:
+        sequences[0][b'direction']=b'forward'
+        sequences[0][b'forward_errors']=directmatch[1][0]
+        sequences[0][b'forward_primer']=directmatch[0].raw
+        sequences[0][b'forward_match']=match.seq
+        
+    else:
+        sequences[0][b'direction']=b'reverse'
+        sequences[0][b'reverse_errors']=directmatch[1][0]
+        sequences[0][b'reverse_primer']=directmatch[0].raw
+        sequences[0][b'reverse_match']=match.seq
+
+    # Keep only paired reverse primer
+    infos = infos[directmatch[0]]
+    reverse_primer = list(infos.keys())[0]
+    direct_primer = directmatch[0]
+        
+    # If not aligned, look for other match in already computed matches (choose the one that makes the biggest amplicon)
+    if not_aligned:
+        i=1
+        # TODO comment
+        while i<len(all_direct_matches) and \
+            (all_direct_matches[i][1] is None or \
+             all_direct_matches[i][0].forward == directmatch[0].forward or \
+             all_direct_matches[i][0] == directmatch[0] or \
+             reverse_primer != all_direct_matches[i][0]) :
+            i+=1
+        if i < len(all_direct_matches):
+            reversematch = all_direct_matches[i]
+        else:
+            reversematch = None
+        
+    # Cut reverse primer out of 1st matched seq if it contains it, because if it's also in the other sequence, the next step will "choose" only the one on the other sequence
+    if not_aligned:
+        # do it on same seq
+        if first_match_first_seq:
+            r = reverse_primer.revcomp(sequences[0])
+        else:
+            r = reverse_primer.revcomp(sequences[1]) 
+        if r is not None: # found
+            if first_match_first_seq :
+                sequences[0] = sequences[0][:r[1]]
+            else:
+                sequences[1] = sequences[1][:r[1]]
+                sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq      # used by alignpairedend tool
+                sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality   # used by alignpairedend tool
+        # do the same on the other seq
+        if first_match_first_seq: 
+            r = direct_primer.revcomp(sequences[1])
+        else:
+            r = direct_primer.revcomp(sequences[0])
+        if r is not None: # found
+            if first_match_first_seq:
+                sequences[1] = sequences[1][:r[1]]
+            else:
+                sequences[0] = sequences[0][:r[1]] 
+                sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq
+                sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality
+    
+    
+    # Look for other primer in the other direction on the sequence, or
+    # If sequences are not already aligned and reverse primer not found in most likely sequence (the one without the forward primer), try matching on the same sequence than the first match (primer in the other direction)
+    if not not_aligned or (not_aligned and (reversematch is None or reversematch[1] is None)):
+        if not_aligned and first_match_first_seq:
+            seq_to_match = sequences[1]
+        else:
+            seq_to_match = sequences[0]
+        reversematch = []
+        # Compute begin
+        #begin=directmatch[1][2]+1  # end of match + 1 on the same sequence -- No, already cut out forward primer        
+        # Try reverse matching on the other sequence:
+        new_seq = True
+        pattern = 0
+        for p in infos:
+            if pattern == MAX_PATTERN:
+                new_seq = True
+                pattern = 0
+            if not_aligned:
+                primer=p.revcomp
+            else:
+                primer=p
+            # Saving original primer as 4th member of the tuple to serve as correct key in infos dict even if it might have been reversed complemented
+            # (3rd member already used by directmatch)
+            reversematch.append((primer, primer(seq_to_match, same_sequence=not new_seq, pattern=pattern, begin=0), None, p))
+            new_seq = False
+            pattern+=1
+        # Choose match closer to the end of the sequence
+        reversematch = sorted(reversematch, key=sortReverseMatch, reverse=True)
+        all_reverse_matches = reversematch
+        reversematch = reversematch[0] if reversematch[0][1] is not None else None
+        
+    if reversematch is None and None not in infos:
+        if directmatch[0].forward:
+            message = b'No reverse primer match'
+        else:
+            message = b'No direct primer match'
+        sequences[0][b'error']=message
+        return False, sequences[0]
+    
+    if reversematch is None:
+        sequences[0][b'status']=b'partial'
+        
+        if directmatch[0].forward:
+            tags=(directmatch[1][3],None)
+        else:
+            tags=(None,directmatch[1][3])
+            
+        samples = infos[None]
+        
+    else:
+        sequences[0][b'status']=b'full'
+        
+        if not not_aligned or first_match_first_seq:
+            match = sequences[0][reversematch[1][1]:reversematch[1][2]]
+        else:
+            match = sequences[1][reversematch[1][1]:reversematch[1][2]]
+        
+        match = match.reverse_complement
+        
+        if not not_aligned:
+            sequences[0] = sequences[0][0:reversematch[1][1]]
+        elif first_match_first_seq:
+            sequences[1] = sequences[1][reversematch[1][2]:]
+            if not directmatch[0].forward:
+                sequences[1] = sequences[1].reverse_complement
+            sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq      # used by alignpairedend tool
+            sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality   # used by alignpairedend tool
+        else:
+            sequences[0] = sequences[0][reversematch[1][2]:]
+            
+        if directmatch[0].forward:
+            tags=(directmatch[1][3], reversematch[1][3])
+            sequences[0][b'reverse_errors'] = reversematch[1][0]
+            sequences[0][b'reverse_primer'] = reversematch[0].raw
+            sequences[0][b'reverse_match'] = match.seq
+        
+        else:
+            tags=(reversematch[1][3], directmatch[1][3])
+            sequences[0][b'forward_errors'] = reversematch[1][0]
+            sequences[0][b'forward_primer'] = reversematch[0].raw
+            sequences[0][b'forward_match'] = match.seq
+                
+        if tags[0] is not None:
+            sequences[0][b'forward_tag'] = tags[0]
+        if tags[1] is not None:
+            sequences[0][b'reverse_tag'] = tags[1]
+
+        samples = infos[reversematch[3]]
+        
+    if not directmatch[0].forward:
+        sequences[0] = sequences[0].reverse_complement
+        sequences[0][b'reversed'] = True   # used by the alignpairedend tool (in kmer_similarity.c)
+    else:
+        sequences[0][b'reversed'] = False   # used by the alignpairedend tool (in kmer_similarity.c)
+
+    sample=None
+    if not no_tags:
+        if tags[0] is not None:                                    # Direct  tag known
+            if tags[1] is not None:                                # Reverse tag known
+                sample = samples.get(tags, None)             
+            else:                                                   # Only direct tag known
+                s=[samples[x] for x in samples if x[0]==tags[0]]
+                if len(s)==1:
+                    sample=s[0]
+                elif len(s)>1:
+                    sequences[0][b'error']=b'Did not found reverse tag'
+                    return False, sequences[0]
+                else:
+                    sample=None
+        else: 
+            if tags[1] is not None:                                 # Only reverse tag known
+                s=[samples[x] for x in samples if x[1]==tags[1]]
+                if len(s)==1:
+                    sample=s[0]
+                elif len(s)>1:
+                    sequences[0][b'error']=b'Did not found forward tag'
+                    return False, sequences[0]
+                else:
+                    sample=None
+        
+        if sample is None:
+            sequences[0][b'error']=b"No sample with that tag combination"
+            return False, sequences[0]
+    
+        sequences[0].update(sample)
+    
+    if not not_aligned:
+        sequences[0][b'seq_length']=len(sequences[0])
+    
+    return True, sequences[0]
+
+
+def run(config):
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi ngsfilter")
+
+    assert config['ngsfilter']['info_view'] is not None, "Option -t must be specified"
+
+    # Open the input
+    
+    forward = None
+    reverse = None
+    input = None
+    not_aligned = False
+    
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not open input reads")
+    if input[2] != View_NUC_SEQS:
+        raise NotImplementedError('obi ngsfilter only works on NUC_SEQS views')
+    i_dms = input[0]
+    
+    if "reverse" in config["ngsfilter"]:
+        
+        forward = input[1]        
+        
+        rinput = open_uri(config["ngsfilter"]["reverse"])
+        if rinput is None:
+            raise Exception("Could not open reverse reads")
+        if rinput[2] != View_NUC_SEQS:
+            raise NotImplementedError('obi ngsfilter only works on NUC_SEQS views')
+        
+        reverse = rinput[1]
+    
+        if len(forward) != len(reverse):
+            raise Exception("Error: the number of forward and reverse reads are different")
+        
+        entries = [forward, reverse]
+        not_aligned = True
+
+        input_dms_name = [forward.dms.name, reverse.dms.name]
+        input_view_name = [forward.name, reverse.name]
+    
+    else:
+        entries = input[1]
+        input_dms_name = [entries.dms.name]
+        input_view_name = [entries.name]
+
+    
+    if not_aligned:
+        entries_len = len(forward)
+    else:
+        entries_len = len(entries)
+    
+    # Open the output
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      newviewtype=View_NUC_SEQS)
+    
+    if output is None:
+        raise Exception("Could not create output view")
+    
+    o_dms = output[0]
+    output_0 = output[0]
+    o_view = output[1]
+    
+    # If stdout output, create a temporary view in the input dms that will be deleted afterwards.
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view = View_NUC_SEQS.new(i_dms, o_view_name)
+
+    # Open the view containing the informations about the tags and the primers
+    info_input = open_uri(config['ngsfilter']['info_view'])
+    if info_input is None:
+        raise Exception("Could not read the view containing the informations about the tags and the primers")
+    info_view = info_input[1]
+    input_dms_name.append(info_input[0].name)   
+    input_view_name.append(info_input[1].name)
+
+    # Open the unidentified view
+    if 'unidentified' in config['ngsfilter'] and config['ngsfilter']['unidentified'] is not None:  # TODO keyError if undefined problem
+        unidentified_input = open_uri(config['ngsfilter']['unidentified'],
+                                      input=False,
+                                      newviewtype=View_NUC_SEQS)
+        if unidentified_input is None:
+            raise Exception("Could not open the view containing the unidentified reads")
+        unidentified = unidentified_input[1]
+    else:
+        unidentified = None
+        
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(entries_len, config)
+    else:
+        pb = None
+
+    # Check and store primers and tags
+    try:
+        infos, primer_list = read_info_view(info_view, max_errors=config['ngsfilter']['error'], verbose=False, not_aligned=not_aligned)   # TODO obi verbose option
+    except RollbackException, e:
+        if unidentified is not None:
+            raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
+        else:
+            raise RollbackException("obi ngsfilter error, rollbacking view: "+str(e), o_view)
+    
+    aligner = Primer_search(primer_list, config['ngsfilter']['error'])
+    
+    for p in infos:
+        p.aligner = aligner
+        for paired_p in infos[p]:
+            paired_p.aligner = aligner
+            if paired_p.revcomp is not None:
+                paired_p.revcomp.aligner = aligner
+    
+    if not_aligned:   # create columns used by alignpairedend tool
+        Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
+        Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
+        
+        if unidentified is not None:
+            Column.new_column(unidentified, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
+            Column.new_column(unidentified, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=unidentified[REVERSE_SEQUENCE_COLUMN].version)
+    
+    g = 0
+    u = 0
+    i = 0
+    no_tags = config['ngsfilter']['notags']
+    try:
+        for i in range(entries_len):
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
+            if not_aligned:
+                modseq = [Nuc_Seq.new_from_stored(forward[i]), Nuc_Seq.new_from_stored(reverse[i])]
+            else:
+                modseq = [Nuc_Seq.new_from_stored(entries[i])]
+            good, oseq = annotate(modseq, infos, no_tags)
+            if good:
+                o_view[g].set(oseq.id, oseq.seq, definition=oseq.definition, quality=oseq.quality, tags=oseq)
+                g+=1
+            elif unidentified is not None:
+                # Untrim sequences (put original back)
+                if len(modseq) > 1:
+                    oseq[REVERSE_SEQUENCE_COLUMN] = reverse[i].seq
+                    oseq[REVERSE_QUALITY_COLUMN] = reverse[i].quality
+                    unidentified[u].set(oseq.id, forward[i].seq, definition=oseq.definition, quality=forward[i].quality, tags=oseq)
+                else:
+                    unidentified[u].set(oseq.id, entries[i].seq, definition=oseq.definition, quality=entries[i].quality, tags=oseq)
+                u+=1
+    except Exception, e:
+        if unidentified is not None:
+            raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
+        else:
+            raise RollbackException("obi ngsfilter error, rollbacking view: "+str(e), o_view)
+    
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "ngsfilter", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    if unidentified is not None:
+        unidentified.write_config(config, "ngsfilter", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+        # Add comment about unidentified seqs
+        unidentified.comments["info"] = "View containing sequences categorized as unidentified by the ngsfilter command"
+    o_dms.record_command_line(command_line)
+    
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # If stdout output, delete the temporary result view in the input DMS
+    if type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+
+    i_dms.close(force=True)
+    o_dms.close(force=True)
+    info_input[0].close(force=True)
+    if unidentified is not None:
+        unidentified_input[0].close(force=True)
+    aligner.free()
+
+    logger("info", "Done.")

python/obitools3/commands/rm.pyx

@@ -0,0 +1,87 @@
+#cython: language_level=3
+
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.dms import DMS
+from obitools3.apps.optiongroups import addMinimalInputOption
+from obitools3.dms.view.view cimport View
+from obitools3.utils cimport tostr
+import os
+import shutil
+ 
+__title__="Delete a view"
+
+
+def addOptions(parser):    
+    addMinimalInputOption(parser)
+
+def run(config):
+
+    DMS.obi_atexit()
+    
+    logger("info", "obi rm")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input")
+    
+    # Check that it's a view
+    if isinstance(input[1], View) :
+        view = input[1]
+    else: 
+        raise NotImplementedError()
+    
+    dms = input[0]
+    
+    # Get the path to the view file to remove
+    path = dms.full_path  # dms path
+    view_path=path+b"/VIEWS/"
+    view_path+=view.name
+    view_path+=b".obiview"
+    
+    to_remove = {}
+    # For each column:
+    for col_alias in view.keys():
+        col = view[col_alias]
+        col_name = col.original_name
+        col_version = col.version
+        col_type = col.data_type
+        col_ref = (col_name, col_version)
+        # build file name and AVL file names
+        col_file_name = f"{tostr(path)}/{tostr(col.original_name)}.obicol/{tostr(col.original_name)}@{col.version}.odc"
+        if col_type in [b'OBI_CHAR', b'OBI_QUAL', b'OBI_STR', b'OBI_SEQ']:
+            avl_file_name = f"{tostr(path)}/OBIBLOB_INDEXERS/{tostr(col.original_name)}_{col.version}_indexer"
+        else:
+            avl_file_name = None
+        to_remove[col_ref] = [col_file_name, avl_file_name]
+    
+    # For each view:
+    do_not_remove = []
+    for vn in dms:
+        v = dms[vn]
+        # ignore the one being deleted
+        if v.name != view.name:
+            # check that none of the column is referenced, if referenced, remove from list to remove
+            cols = [(v[c].original_name, v[c].version) for c in v.keys()]
+            for col_ref in to_remove:
+                if col_ref in cols:
+                    do_not_remove.append(col_ref)
+    
+    for nr in do_not_remove:
+        to_remove.pop(nr)
+    
+    # Close the view and the DMS
+    view.close()
+    input[0].close(force=True)
+    
+    #print(to_remove)
+    
+    # rm AFTER view and DMS close
+    os.remove(view_path)
+    for col in to_remove:
+        os.remove(to_remove[col][0])
+        if to_remove[col][1] is not None:
+            shutil.rmtree(to_remove[col][1])
+        
+        

python/obitools3/commands/sort.pyx

@@ -0,0 +1,168 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
+
+from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
+                                         OBI_CHAR, \
+                                         OBI_FLOAT, \
+                                         OBI_INT, \
+                                         OBI_QUAL, \
+                                         OBI_SEQ, \
+                                         OBI_STR, \
+                                         OBIBool_NA, \
+                                         OBIChar_NA, \
+                                         OBIFloat_NA, \
+                                         OBIInt_NA
+
+import time
+import sys
+from cpython.exc cimport PyErr_CheckSignals
+from io import BufferedWriter
+
+ 
+NULL_VALUE = {OBI_BOOL: OBIBool_NA, 
+              OBI_CHAR: OBIChar_NA, 
+              OBI_FLOAT: OBIFloat_NA,
+              OBI_INT: OBIInt_NA,
+              OBI_QUAL: [],
+              OBI_SEQ: b"",
+              OBI_STR: b""}
+ 
+
+__title__="Sort view lines according to the value of a given attribute"
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi sort specific options')
+
+    group.add_argument('--key', '-k',
+                       action="append", dest="sort:keys",
+                       metavar='<TAG NAME>',
+                       default=[],
+                       type=str,
+                       help="Attribute used to sort the sequence records.")
+
+    group.add_argument('--reverse', '-r',
+                       action="store_true", dest="sort:reverse",
+                       default=False,
+                       help="Sort in reverse order.")
+
+
+def line_cmp(line, key, pb): 
+    pb
+    if line[key] is None:
+        return NULL_VALUE[line.view[key].data_type_int]
+    else:
+        return line[key]
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi sort")
+
+    # Open the input
+    input = open_uri(config["obi"]["inputURI"])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    final_o_view_name = output[1]
+    
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(i_view), config)
+    else:
+        pb = None
+
+    keys = config['sort']['keys']
+        
+    selection = Line_selection(i_view)
+    
+    for i in range(len(i_view)):  # TODO special function?
+        PyErr_CheckSignals()
+        selection.append(i)
+    
+    for k in keys:  # TODO order?
+        PyErr_CheckSignals()
+        if pb is not None:
+            selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
+        else:
+            selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, None), reverse=config['sort']['reverse'])
+    
+    if pb is not None:
+        pb(len(i_view), force=True)
+        print("", file=sys.stderr)
+
+    # Create output view with the sorted line selection
+    try:
+        o_view = selection.materialize(o_view_name)
+    except Exception, e:
+        raise RollbackException("obi sort error, rollbacking view: "+str(e), o_view)
+
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[input[0].name]
+    input_view_name=[input[1].name]
+    o_view.write_config(config, "sort", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
+
+    # If input and output DMS are not the same, export the temporary view to the output DMS
+    # and delete the temporary view in the input DMS
+    if i_dms != o_dms:
+        o_view.close()
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+        o_view = o_dms[final_o_view_name]
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close(force=True)
+
+    i_dms.close(force=True)
+
+    logger("info", "Done.")

python/obitools3/commands/split.pyx

@@ -0,0 +1,105 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes
+
+import sys
+from cpython.exc cimport PyErr_CheckSignals
+
+ 
+__title__="Split"
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group("obi split specific options")
+ 
+    group.add_argument('-p','--prefix',
+                       action="store", dest="split:prefix",
+                       metavar="<PREFIX>",
+                       help="Prefix added to each subview name (included undefined)")
+
+    group.add_argument('-t','--tag-name',
+                       action="store", dest="split:tagname",
+                       metavar="<TAG_NAME>",
+                       help="Attribute/tag used to split the input")
+      
+    group.add_argument('-u','--undefined',
+                       action="store", dest="split:undefined",
+                       default=b'UNDEFINED',
+                       metavar="<VIEW_NAME>",
+                       help="Name of the view where undefined sequenced are stored (will be PREFIX_VIEW_NAME)")
+
+
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi split")
+
+    # Open the input
+    input = open_uri(config["obi"]["inputURI"])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(i_view), config)
+    else:
+        pb = None
+    
+    tag_to_split = config["split"]["tagname"]
+    undefined = tobytes(config["split"]["undefined"])
+    selections = {}
+    
+    # Go through input view and split
+    for i in range(len(i_view)):
+        PyErr_CheckSignals()
+        if pb is not None:
+            pb(i)
+        line = i_view[i]
+        if tag_to_split not in line or line[tag_to_split] is None or len(line[tag_to_split])==0:
+            value = undefined
+        else:
+            value = line[tag_to_split]
+        if value not in selections:
+            selections[value] = Line_selection(i_view)
+        selections[value].append(i)
+        
+    if pb is not None:
+        pb(len(i_view), force=True)
+        print("", file=sys.stderr)
+
+    # Create output views with the line selection
+    try:
+        for cat in selections:
+            o_view_name = config["split"]["prefix"].encode()+cat
+            o_view = selections[cat].materialize(o_view_name)
+            # Save command config in View and DMS comments
+            command_line = " ".join(sys.argv[1:])
+            input_dms_name=[input[0].name]
+            input_view_name=[input[1].name]
+            if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+                input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+                input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+            o_view.write_config(config, "split", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+            o_view.close()
+    except Exception, e:
+        raise RollbackException("obi split error, rollbacking view: "+str(e), o_view)
+
+    i_dms.record_command_line(command_line)
+    i_dms.close(force=True)
+
+    logger("info", "Done.")
+

python/obitools3/commands/stats.pyx

@@ -0,0 +1,296 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.dms.capi.obiview cimport COUNT_COLUMN
+from obitools3.utils cimport tostr
+
+from functools import reduce
+import math
+import time
+import sys
+from cpython.exc cimport PyErr_CheckSignals
+
+
+__title__="Compute basic statistics for attribute values"
+
+'''
+`obi stats` computes basic statistics for attribute values of sequence records.
+The sequence records can be categorized or not using one or several ``-c`` options.
+By default, only the number of sequence records and the total count are computed for each category. 
+Additional statistics can be computed for attribute values in each category, such as:
+
+    - minimum value (``-m`` option) 
+    - maximum value (``-M`` option) 
+    - mean value (``-a`` option) 
+    - variance (``-v`` option) 
+    - standard deviation (``-s`` option)
+    
+The result is a contingency table with the different categories in rows, and the 
+computed statistics in columns. 
+'''
+
+
+# TODO: when is the taxonomy possibly used?
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+
+    group=parser.add_argument_group('obi stats specific options')
+
+    group.add_argument('-c','--category-attribute',
+                       action="append", dest="stats:categories",
+                             metavar="<Attribute Name>",
+                             default=[],
+                             help="Attribute used to categorize the records.")
+    
+    group.add_argument('-m','--min',
+                       action="append", dest="stats:minimum",
+                       metavar="<Attribute Name>",
+                       default=[],
+                       help="Compute the minimum value of attribute for each category.")
+    
+    group.add_argument('-M','--max',
+                       action="append", dest="stats:maximum",
+                       metavar="<Attribute Name>",
+                       default=[],
+                       help="Compute the maximum value of attribute for each category.")
+
+    group.add_argument('-a','--mean',
+                       action="append", dest="stats:mean",
+                       metavar="<Attribute Name>",
+                       default=[],
+                       help="Compute the mean value of attribute for each category.")
+
+    group.add_argument('-v','--variance',
+                       action="append", dest="stats:var",
+                       metavar="<Attribute Name>",
+                       default=[],
+                       help="Compute the variance of attribute for each category.")
+
+    group.add_argument('-s','--std-dev',
+                       action="append", dest="stats:sd",
+                       metavar="<Attribute Name>",
+                       default=[],
+                       help="Compute the standard deviation of attribute for each category.")
+
+
+def statistics(values, attributes, func):
+    
+    stat={}
+    lstat={}
+    
+    for var in attributes:
+        if var in values:
+            stat[var]={}
+            lstat[var]=0
+            for c in values[var]:
+                v = values[var][c]
+                m = func(v)
+                stat[var][c]=m
+                lm=len(str(m))
+                if lm > lstat[var]:
+                    lstat[var]=lm
+                
+    return stat, lstat
+
+
+def minimum(values, options):
+    return statistics(values, options['minimum'], min)
+    
+
+def maximum(values, options):
+    return statistics(values, options['maximum'], max)
+
+
+def mean(values, options):
+    def average(v):
+        s = reduce(lambda x,y:x+y,v,0)
+        return float(s)/len(v)
+    return statistics(values, options['mean'], average)
+
+
+def variance(v):
+    if len(v)==1: 
+        return 0
+    s = reduce(lambda x,y:(x[0]+y,x[1]+y**2),v,(0.,0.))
+    var = round(s[1]/(len(v)-1) - s[0]**2/len(v)/(len(v)-1), 5) # round to go around shady python rounding stuff when var is actually 0
+    if var == -0.0: # then fix -0 to +0 if was rounded to -0
+        var = 0.0
+    return var
+
+
+def varpop(values, options):
+    return statistics(values, options['var'], variance)
+    
+
+def sd(values, options):
+    def stddev(v):
+        return math.sqrt(variance(v))
+    return statistics(values, options['sd'], stddev)
+
+ 
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi stats")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_view = input[1]
+
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        taxo_uri = open_uri(config['obi']['taxoURI'])
+        if taxo_uri is None or taxo_uri[2] == bytes:
+            raise Exception("Couldn't open taxonomy")
+        taxo = taxo_uri[1]
+    else :
+        taxo = None
+
+    statistics = set(config['stats']['minimum']) | set(config['stats']['maximum']) | set(config['stats']['mean']) | set(config['stats']['var']) | set(config['stats']['sd'])
+    total = 0
+    catcount={}
+    totcount={}
+    values={}
+    lcat=0
+    
+    # Initialize the progress bar
+    pb = ProgressBar(len(i_view), config)
+    
+    for i in range(len(i_view)):
+        PyErr_CheckSignals()
+        pb(i)
+        line = i_view[i]
+        
+        category = []
+        for c in config['stats']['categories']:
+            try:
+                if taxo is not None:
+                    loc_env = {'sequence': line, 'line': line, 'taxonomy': taxo}
+                else:
+                    loc_env = {'sequence': line, 'line': line}
+
+                v = eval(c, loc_env, line)
+                
+                lv=len(str(v))
+                if lv > lcat:
+                    lcat=lv
+                category.append(v)
+            except:
+                category.append(None)
+                if 4 > lcat:
+                    lcat=4
+
+        category=tuple(category)
+        catcount[category]=catcount.get(category,0)+1
+        try: 
+            totcount[category]=totcount.get(category,0)+line[COUNT_COLUMN]
+        except KeyError:
+            totcount[category]=totcount.get(category,0)+1
+        for var in statistics:
+            if var in line and line[var] is not None:
+                v = line[var]
+                if var not in values:
+                    values[var]={}
+                if category not in values[var]:
+                    values[var][category]=[]
+                values[var][category].append(v)    
+
+    pb(i, force=True)
+    print("", file=sys.stderr)
+    
+    mini, lmini = minimum(values, config['stats'])
+    maxi, lmaxi = maximum(values, config['stats'])
+    avg, lavg = mean(values, config['stats'])
+    varp, lvarp = varpop(values, config['stats'])
+    sigma, lsigma = sd(values, config['stats'])
+
+    pcat = "%%-%ds" % lcat
+    if config['stats']['minimum']:
+        minvar= "min_%%-%ds" % max(len(x) for x in config['stats']['minimum'])
+    else:
+        minvar= "%s"
+        
+    if config['stats']['maximum']:
+        maxvar= "max_%%-%ds" % max(len(x) for x in config['stats']['maximum'])
+    else:
+        maxvar= "%s"
+        
+    if config['stats']['mean']:
+        meanvar= "mean_%%-%ds" % max(len(x) for x in config['stats']['mean'])
+    else:
+        meanvar= "%s"
+        
+    if config['stats']['var']:
+        varvar= "var_%%-%ds" % max(len(x) for x in config['stats']['var'])
+    else:
+        varvar= "%s"
+        
+    if config['stats']['sd']:
+        sdvar= "sd_%%-%ds" % max(len(x) for x in config['stats']['sd'])
+    else:
+        sdvar= "%s"
+        
+    hcat = ""
+    
+    for x in config['stats']['categories']:
+        hcat += pcat % x
+        hcat += "\t"
+    
+    for x in config['stats']['minimum']:
+        hcat += minvar % x
+        hcat += "\t"
+
+    for x in config['stats']['maximum']:
+        hcat += maxvar % x
+        hcat += "\t"
+
+    for x in config['stats']['mean']:
+        hcat += meanvar % x
+        hcat += "\t"
+    
+    for x in config['stats']['var']:
+        hcat += varvar % x
+        hcat += "\t"
+
+    for x in config['stats']['sd']:
+        hcat += sdvar % x
+        hcat += "\t"
+
+    hcat += "count\ttotal" 
+    
+    print(hcat)
+    sorted_stats = sorted(catcount.items(), key = lambda kv:(totcount[kv[0]]), reverse=True)
+    for i in range(len(sorted_stats)):
+        c = sorted_stats[i][0]
+        for v in c:
+            if type(v) == bytes:
+                print(pcat % tostr(v)+"\t", end="")
+            else:
+                print(pcat % str(v)+"\t", end="")
+        for m in config['stats']['minimum']:
+            print((("%%%dd" % lmini[m]) % mini[m][c])+"\t", end="")
+        for m in config['stats']['maximum']:
+            print((("%%%dd" % lmaxi[m]) % maxi[m][c])+"\t", end="")
+        for m in config['stats']['mean']:
+            print((("%%%df" % lavg[m]) % avg[m][c])+"\t", end="")
+        for m in config['stats']['var']:
+            print((("%%%df" % lvarp[m]) % varp[m][c])+"\t", end="")
+        for m in config['stats']['sd']:
+            print((("%%%df" % lsigma[m]) % sigma[m][c])+"\t", end="")
+        print("%d" %catcount[c]+"\t", end="")
+        print("%d" %totcount[c]+"\t")
+
+    input[0].close(force=True)
+    
+    logger("info", "Done.")

python/obitools3/commands/tail.pyx

@@ -0,0 +1,130 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
+
+import time
+import sys
+from cpython.exc cimport PyErr_CheckSignals
+from io import BufferedWriter
+
+
+__title__="Keep the N last lines of a view"
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi tail specific options')
+
+    group.add_argument('-n', '--sequence-count',
+                       action="store", dest="tail:count",
+                       metavar='<N>',
+                       default=10,
+                       type=int,
+                       help="Number of last records to keep.")
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi tail")
+
+    # Open the input
+    input = open_uri(config["obi"]["inputURI"])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    final_o_view_name = output[1]
+    
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+    else:
+        o_view_name = final_o_view_name
+    
+    start = max(len(i_view) - config['tail']['count'], 0)
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(i_view) - start, config)
+    else:
+        pb = None
+        
+    selection = Line_selection(i_view)
+    
+    for i in range(start, len(i_view)):
+        PyErr_CheckSignals()
+        if pb is not None:
+            pb(i)
+        selection.append(i)
+
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
+
+    # Save command config in View comments
+    command_line = " ".join(sys.argv[1:])
+    comments = View.get_config_dict(config, "tail", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
+
+    # Create output view with the line selection
+    try:
+        o_view = selection.materialize(o_view_name)
+    except Exception, e:
+        raise RollbackException("obi tail error, rollbacking view: "+str(e), o_view)
+
+    # Save command config in DMS comments
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "tail", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
+    o_dms.record_command_line(command_line)
+
+    # If input and output DMS are not the same, export the temporary view to the output DMS
+    # and delete the temporary view in the input DMS
+    if i_dms != o_dms:
+        o_view.close()
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+        o_view = o_dms[final_o_view_name]
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close(force=True)
+    i_dms.close(force=True)
+    
+    logger("info", "Done.")

python/obitools3/commands/taxonomy.pyx

@@ -0,0 +1,230 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
+from obitools3.dms.view import RollbackException
+from obitools3.dms.column.column cimport Column
+from functools import reduce
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes, tostr
+from io import BufferedWriter
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_INT
+from obitools3.dms.capi.obitaxonomy cimport MIN_LOCAL_TAXID
+import time
+import math
+import sys
+
+from cpython.exc cimport PyErr_CheckSignals
+
+
+__title__="Add taxa with a new generated taxid to an NCBI taxonomy database"
+
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
+
+    group=parser.add_argument_group('obi taxonomy specific options')
+
+    group.add_argument('-n', '--taxon-name-tag',
+                       action="store",
+                       dest="taxonomy:taxon_name_tag",
+                       metavar="<SCIENTIFIC_NAME_TAG>",
+                       default=b"SCIENTIFIC_NAME",
+                       help="Name of the tag giving the scientific name of the taxon "
+                            "(default: 'SCIENTIFIC_NAME').")
+
+#    group.add_argument('-g', '--try-genus-match',
+#                     action="store_true", dest="taxonomy:try_genus_match",
+#                     default=False,
+#                     help="Try matching the first word of <SCIENTIFIC_NAME_TAG> when can't find corresponding taxid for a taxon. "
+#                          "If there is a match it is added in the 'parent_taxid' tag. (Can be used by 'obi taxonomy' to add the taxon under that taxid).")
+
+    group.add_argument('-a', '--restricting-ancestor',
+                       action="store",
+                       dest="taxonomy:restricting_ancestor",
+                       metavar="<RESTRICTING_ANCESTOR>",
+                       default=None,
+                       help="Enables to restrict the addition of taxids under an ancestor specified by its taxid.")
+
+    group.add_argument('-t', '--taxid-tag',
+                       action="store",
+                       dest="taxonomy:taxid_tag",
+                       metavar="<TAXID_TAG>",
+                       default=b"TAXID",
+                       help="Name of the tag to store the new taxid "
+                            "(default: 'TAXID').")
+
+    group.add_argument('-l', '--log-file',
+                       action="store",
+                       dest="taxonomy:log_file",
+                       metavar="<LOG_FILE>",
+                       default='',
+                       help="Path to a log file to write informations about added taxids.")
+
+
+def run(config):
+
+    DMS.obi_atexit()
+
+    logger("info", "obi taxonomy")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_dms = input[0]
+    i_view = input[1]
+    i_view_name = input[1].name
+
+    # Open the output: only the DMS, as the output view is going to be created by cloning the input view
+    # (could eventually be done via an open_uri() argument)
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    output_0 = output[0]
+    o_view_name = output[1]
+
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms: # Making sure view name is unique in output DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        imported_view_name = o_view_name
+
+    # If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
+    # (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
+    if i_dms != o_dms:
+        imported_view_name = i_view_name
+        i=0
+        while imported_view_name in o_dms:  # Making sure view name is unique in output DMS
+            imported_view_name = i_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
+        i_view = o_dms[imported_view_name]
+
+    # Clone output view from input view
+    o_view = i_view.clone(o_view_name)
+    if o_view is None:
+        raise Exception("Couldn't create output view")
+    i_view.close()
+
+    # Open taxonomy
+    taxo_uri = open_uri(config['obi']['taxoURI'])
+    if taxo_uri is None or taxo_uri[2] == bytes:
+        raise Exception("Couldn't open taxonomy")
+    taxo = taxo_uri[1]
+
+    # Initialize the progress bar
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(o_view), config)
+    else:
+        pb = None
+
+    try:
+        if config['taxonomy']['log_file']:
+            logfile = open(config['taxonomy']['log_file'], 'w')
+        else:
+            logfile = sys.stdout
+        if 'restricting_ancestor' in config['taxonomy']:
+            res_anc = int(config['taxonomy']['restricting_ancestor'])
+        else:
+            res_anc = None
+        taxid_column_name = config['taxonomy']['taxid_tag']
+        parent_taxid_column_name = "PARENT_TAXID" # TODO macro
+        taxon_name_column_name = config['taxonomy']['taxon_name_tag']
+        taxid_column = Column.new_column(o_view, taxid_column_name, OBI_INT)
+        if parent_taxid_column_name in o_view:
+            parent_taxid_column = o_view[parent_taxid_column_name]
+        else:
+            parent_taxid_column = None
+        #parent_taxid_column = Column.new_column(o_view, parent_taxid_column_name, OBI_INT)
+        taxon_name_column = o_view[taxon_name_column_name]
+
+        for i in range(len(o_view)):
+            PyErr_CheckSignals()
+            #if pb is not None:
+            #    pb(i)
+            taxon_name = taxon_name_column[i]
+            taxon = taxo.get_taxon_by_name(taxon_name, res_anc)
+            if taxon is not None:
+                taxid_column[i] = taxon.taxid
+                if logfile:
+                    print(f"Found taxon '{tostr(taxon_name)}' already existing with taxid {taxid_column[i]}", file=logfile)
+            else: # try finding genus or other parent taxon from the first word
+                #print(i, o_view[i].id)
+                if parent_taxid_column is not None and parent_taxid_column[i] is not None:
+                    taxid_column[i] = taxo.add_taxon(taxon_name, 'species', parent_taxid_column[i])
+                    if logfile:
+                        print(f"Adding taxon '{tostr(taxon_name)}' under provided parent {parent_taxid_column[i]} with taxid {taxid_column[i]}", file=logfile)
+                else:
+                    taxon_name_sp = taxon_name.split(b" ")
+                    taxon = taxo.get_taxon_by_name(taxon_name_sp[0], res_anc)
+                    if taxon is not None:
+                        parent_taxid_column[i] = taxon.taxid
+                        taxid_column[i] = taxo.add_taxon(taxon_name, 'species', taxon.taxid)
+                        if logfile:
+                            print(f"Adding taxon '{tostr(taxon_name)}' under '{tostr(taxon.name)}' ({taxon.taxid}) with taxid {taxid_column[i]}", file=logfile)
+                    else:
+                        taxid_column[i] = taxo.add_taxon(taxon_name, 'species', res_anc)
+                        if logfile:
+                            print(f"Adding taxon '{tostr(taxon_name)}' under provided restricting ancestor {res_anc} with taxid {taxid_column[i]}", file=logfile)
+
+        taxo.write(taxo.name, update=True)
+        
+    except Exception, e:
+        raise RollbackException("obi taxonomy error, rollbacking view: "+str(e), o_view)
+
+    #if pb is not None:
+    #    pb(i, force=True)
+    #    print("", file=sys.stderr)
+
+    #logger("info", "\nTaxa already in the taxonomy: "+str(found_count)+"/"+str(len(o_view))+" ("+str(round(found_count*100.0/len(o_view), 2))+"%)")
+    #logger("info", "\nParent taxids found: "+str(parent_found_count)+"/"+str(len(o_view))+" ("+str(round(parent_found_count*100.0/len(o_view), 2))+"%)")
+    #logger("info", "\nTaxids not found: "+str(not_found_count)+"/"+str(len(o_view))+" ("+str(round(not_found_count*100.0/len(o_view), 2))+"%)")
+
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[input[0].name]
+    input_view_name=[i_view_name]
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+        input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+    o_view.write_config(config, "taxonomy", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        View.delete_view(o_dms, imported_view_name)
+        o_dms.close(force=True)
+    i_dms.close(force=True)
+
+    logger("info", "Done.")