Patch the way of installing the obi main command

previous commit

.gitignore

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+.DS_Store
+/obitools.test/
+/OBITools3- 1.01.16/
+/OBITools3-0.00.0/
+/build/
+/testpip/
+/toto.obidms/
+/unittests/
+/setup.py.old
+/3_Hornung_testseq.fastq
+/sample/
+/save.temp/
+/obitmp/

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>obitools3</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

.pydevproject

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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?><pydev_project>
+        
+    
+    <pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">python3.6-obitool3</pydev_property>
+        
+    
+    <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python interpreter</pydev_property>
+        
+    
+    <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
+                
+        
+        <path>/${PROJECT_DIR_NAME}/python</path>
+                
+    
+    </pydev_pathproperty>
+        
+
+</pydev_project>

LICENSE

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+
+  CeCILL FREE SOFTWARE LICENSE AGREEMENT
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README.md

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+The `OBITools3`: A package for the management of analyses and data in DNA metabarcoding   
+---------------------------------------------
+
+
+
+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] - <http://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`. Eventually, new versions of `ecoPrimers` (PCR primer design) [3], `ecoPCR` (*in silico* PCR) [4], as well as `Sumatra` (sequence alignment) and `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 3.5`. The `OBITools3` are still in development, and the first functional versions are expected for autumn 2016.    
+
+
+
+**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 2015:n/a–n/a.
+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>

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/conf.py

@@ -33,10 +33,10 @@ extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
-    'sphinx.ext.pngmath',
+    'sphinx.ext.imgmath',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
-#    'breathe',
+    'breathe',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -295,4 +295,6 @@ texinfo_documents = [
 sys.path.append( "breathe/" )
 breathe_projects = { "OBITools3": "doxygen/xml/" }
 breathe_default_project = "OBITools3"
-
+#breathe_projects_source = {
+#     "auto" : ( "../src", ["obidms.h", "obiavl.h"] )
+#     }

doc/source/index.rst

@@ -11,7 +11,7 @@ OBITools3 documentation
 
    Programming guidelines <guidelines>
    Data structures <data>
-
+   Code documentation <code_doc/codedoc>
 
 Indices and tables
 ------------------

doc/source/types.rst

@@ -4,6 +4,7 @@ OBITypes
 
     
 .. image:: ./UML/OBITypes_UML.png
+
 :download:`html version of the OBITypes UML file <UML/OBITypes_UML.class.violet.html>`
 
 

doc/sphinx/.gitignore

@@ -0,0 +1,2 @@
+.DS_Store
+/build_dir.txt

doc/sphinx/build_dir.txt

@@ -1 +0,0 @@
-build/lib.macosx-10.6-intel-3.5

python/.gitignore

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

python/obitools3/apps/arguments.cfiles

@@ -0,0 +1,110 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h
+
+
+
+
+
+
+

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 +1,62 @@
+#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')
+
+    parser.add_argument('--no-progress', dest='%s:progress' % configname, 
+                                       action='store_false', 
+                                       default=None, 
+                        help='Do not print the progress bar during analyzes')
+
+    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.cfiles

@@ -0,0 +1,110 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h
+
+
+
+
+
+
+

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.cfiles

@@ -0,0 +1,110 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h
+
+
+
+
+
+
+

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
+from _curses 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.cfiles

@@ -0,0 +1,110 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h
+
+
+
+
+
+
+

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 +1,272 @@
+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('--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")
+
+    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 __addTabularInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for tabular files")
+
+    group.add_argument('--header',
+                     action="store_true", dest="obi:header",
+                     default=False,
+                     help="First line of tabular file contains column names")
+
+    group.add_argument('--sep',
+                     action="store", dest="obi:sep",
+                     default=None,
+                     type=str,
+                     help="Column separator")
+    
+    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 __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 addTaxonomyOption(optionManager):
+    __addTaxonomyOption(optionManager)
+
+
+def addTaxdumpInputOption(optionManager):
+    __addTaxdumpInputOption(optionManager)
+
+
+def addAllInputOption(optionManager):
+    __addInputOption(optionManager)
+    __addImportInputOption(optionManager)
+    __addTabularInputOption(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 is it is not existing")
+
+    group.add_argument('--max-elts',
+                 action="store", dest="obi:maxelts",
+                 metavar='<N>',
+                 default=1000,
+                 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('--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('--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 addMinimalOutputOption(optionManager):
+    __addOutputOption(optionManager)
+    __addDMSOutputOption(optionManager)
+
+def addExportOutputOption(optionManager):
+    __addOutputOption(optionManager)
+    __addExportOutputOption(optionManager)
+
+
+def addAllOutputOption(optionManager):
+    __addOutputOption(optionManager)
+    __addDMSOutputOption(optionManager)
+    __addExportOutputOption(optionManager)
+

python/obitools3/apps/progress.cfiles

@@ -0,0 +1,110 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h
+
+
+
+
+
+
+

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 seconde=0.1,
+                 cut=False):
+        
+        self.starttime = self.clock()
+        self.lasttime  = self.starttime
+        self.tickcount = <clock_t> (seconde * 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.cfiles

@@ -0,0 +1,110 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h
+
+
+
+
+
+
+

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/align.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

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 +1,274 @@
+#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
+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
+
+import time
+import sys
+
+
+__title__="Aligns one sequence column with itself or two sequence columns"
+
+
+def addOptions(parser):
+   
+   addMinimalInputOption(parser)
+   addMinimalOutputOption(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]
+    o_dms_name = o_dms.name 
+    final_o_view_name = output[1]
+
+    # If 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:
+        temporary_view_name = final_o_view_name
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+    else:
+        o_view_name = final_o_view_name
+        
+    # 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,  \
+                  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()
+
+    # If the input and the output DMS are different, delete the temporary result view in the input DMS
+    if i_dms != o_dms:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    
+    i_dms.close()
+    
+    logger("info", "Done.")
+  

python/obitools3/commands/alignpairedend.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

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 +1,249 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+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.capi.obiview cimport QUALITY_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_QUAL
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+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.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
+
+import sys
+import os
+
+
+__title__="Aligns paired-ended reads"
+
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(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")
+
+    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 (not when using -A option; 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_SEQ_COLUMN_NAME], quality=seqF[REVERSE_QUALITY_COLUMN_NAME])
+            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")
+
+    view = output[1]
+    
+    Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)   #TODO output URI quality option?
+
+    if 'smin' in config['alignpairedend']:
+        smin = config['alignpairedend']['smin']
+    else:
+        smin = 0
+
+    # Initialize the progress bar
+    pb = ProgressBar(entries_len, config, seconde=5)
+    
+    if config['alignpairedend']['trueali']:
+        kmer_ali = False
+        aligner = buildAlignment
+    else :
+        kmer_ali = True
+        if type(entries) == list:
+            forward = entries[0]
+            reverse = entries[1]
+            aligner = Kmer_similarity(forward, view2=reverse, kmer_size=config['alignpairedend']['kmersize'])
+        else:
+            aligner = Kmer_similarity(entries, column2=entries[REVERSE_SEQ_COLUMN_NAME], qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], kmer_size=config['alignpairedend']['kmersize'])
+        
+    ba = alignmentIterator(entries, aligner)
+
+    i = 0
+    for ali in ba:
+        
+        pb(i)
+        
+        consensus = view[i]
+        
+        if not two_views:
+            seqF = entries[i]
+        else:
+            seqF = forward[i]
+                
+        if smin > 0:
+            if (ali.score > smin) :
+                buildConsensus(ali, consensus, seqF)
+            else:
+                if not two_views:
+                    seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality = seqF[REVERSE_QUALITY_COLUMN_NAME])
+                else:
+                    seqR = reverse[i]
+                buildJoinedSequence(ali, seqR, consensus, forward=seqF)
+                
+            consensus[b"smin"] = smin
+        else:
+            buildConsensus(ali, consensus, seqF)
+                
+        if kmer_ali :
+            ali.free()
+    
+        i+=1
+
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
+    if kmer_ali :
+        aligner.free()
+
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    output[0].record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(view), file=sys.stderr)
+    
+    input[0].close()
+    if two_views:
+        rinput[0].close()
+    output[0].close()
+
+    logger("info", "Done.")
+    

python/obitools3/commands/annotate.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

python/obitools3/commands/annotate.pyx

@@ -0,0 +1,382 @@
+#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
+from obitools3.dms.view import RollbackException
+from functools import reduce
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes, str2bytes
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN
+
+import time
+import math 
+import sys
+
+ 
+__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)
+
+    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' in seq:
+                taxid = seq['taxid']
+                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
+                    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,e:       # TODO discuss usefulness of this
+            #    if options.onlyValid:
+            #        raise e
+            #    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,e:
+#                if options.onlyValid:
+#                    raise e
+#                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,e:
+#                if options.onlyValid:
+#                    raise e
+#                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,e:
+#                if options.onlyValid:
+#                    raise e
+#                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:
+#                if options.onlyValid:
+#                    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]
+    o_view_name = output[1]
+    
+    # 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:
+            raise Exception("Couldn't open taxonomy")
+        taxo = taxo_uri[1]
+    else :
+        taxo = None
+
+    # Initialize the progress bar
+    pb = ProgressBar(len(o_view), config, seconde=5)
+
+    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)):
+            pb(i)
+            sequenceTagger(o_view[i])
+
+    except Exception, e:
+        raise RollbackException("obi annotate error, rollbacking view: "+str(e), o_view)
+
+    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)
+    output[0].record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_view), file=sys.stderr)
+
+    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
+    if i_dms != o_dms:
+        View.delete_view(o_dms, imported_view_name)
+        o_dms.close()
+    i_dms.close()
+
+    logger("info", "Done.")

python/obitools3/commands/build_ref_db.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

python/obitools3/commands/build_ref_db.pyx

@@ -0,0 +1,105 @@
+#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
+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
+
+
+__title__="Tag a set of sequences for PCR and sequencing errors identification"
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(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=0.0,
+                      type=float,
+                      help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.00"
+                           " (no threshold).")
+
+
+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]
+    final_o_view_name = output[1]
+    
+    # If 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:
+        temporary_view_name = final_o_view_name
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+    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(tobytes(i_dms_name), 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)
+    
+    # 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, delete the temporary result view in the input DMS
+    if i_dms != o_dms:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    
+    i_dms.close()
+
+    logger("info", "Done.")
+    

python/obitools3/commands/clean.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

python/obitools3/commands/clean.pyx

@@ -0,0 +1,124 @@
+#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
+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
+
+
+__title__="Tag a set of sequences for PCR and sequencing errors identification"
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(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,
+                       default="merged_sample",
+                       help="Name of the tag where sample counts are kept.")
+    
+    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.")
+
+
+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]
+    final_o_view_name = output[1]
+    
+    # If the input and output DMS are not the same, run obiclean creating a temporary view that will be exported to 
+    # the right DMS and deleted in the other afterwards.
+    if i_dms != o_dms:
+        temporary_view_name = final_o_view_name
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+    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 obi_clean(tobytes(i_dms_name), 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'], 1) < 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)
+    
+    # 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, delete the temporary result view in the input DMS
+    if i_dms != o_dms:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    
+    i_dms.close()
+
+    logger("info", "Done.")

python/obitools3/commands/count.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

python/obitools3/commands/count.pyx

@@ -0,0 +1,55 @@
+#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
+
+
+__title__="Counts 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.")
+ 
+    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).")
+
+    
+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]
+
+    count1 = len(entries)
+    count2 = 0
+    
+    if COUNT_COLUMN in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
+        for e in entries:
+            count2+=e[COUNT_COLUMN]
+
+    if COUNT_COLUMN in entries and (config['count']['sequence'] == config['count']['all']):
+        print(count1,count2)
+    elif COUNT_COLUMN in entries and config['count']['all']:
+        print(count2)
+    else:
+        print(count1)

python/obitools3/commands/ecopcr.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

python/obitools3/commands/ecopcr.pyx

@@ -0,0 +1,202 @@
+#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
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.utils cimport tobytes
+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
+
+
+__title__="in silico PCR"
+
+
+# TODO: add option to output unique ids
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(parser)
+
+ 
+    group = parser.add_argument_group('obi ecopcr specific options')
+
+    group.add_argument('--primer1', '-F',
+                       action="store", dest="ecopcr:primer1",
+                       metavar='<PRIMER>',
+                       type=str,
+                       help="Forward primer.")
+
+    group.add_argument('--primer2', '-R',
+                       action="store", dest="ecopcr:primer2",
+                       metavar='<PRIMER>',
+                       type=str,
+                       help="Reverse primer.")
+
+    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-nucs', '-D',
+                       action="store", 
+                       dest="ecopcr:keep-nucs",
+                       metavar="<INTEGER>",
+                       type=int,
+                       default=0,
+                       help="Keeps the specified number of nucleotides on each side of the in silico amplified sequences, "
+                            "(already including the amplified DNA fragment plus the two target sequences of the primers).")
+
+    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]
+    o_dms_name = output[0].name
+    o_view_name = output[1]
+
+    # 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, "ecopcr", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+
+    # TODO: primers in comments?
+
+    if obi_ecopcr(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), \
+                  tobytes(o_dms_name), 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']['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)
+    
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(o_dms[o_view_name]), file=sys.stderr)
+
+    o_dms.close()
+
+    logger("info", "Done.")

python/obitools3/commands/ecotag.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

python/obitools3/commands/ecotag.pyx

@@ -0,0 +1,129 @@
+#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
+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
+
+
+__title__="Taxonomic assignment of sequences"
+
+
+def addOptions(parser):
+
+    addMinimalInputOption(parser)
+    addTaxonomyOption(parser)
+    addMinimalOutputOption(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).")
+
+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]
+
+    # 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]
+    final_o_view_name = output[1]
+    
+    # If the input and output DMS are not the same, run ecotag creating a temporary view that will be exported to 
+    # the right DMS and deleted in the other afterwards.
+    if i_dms != o_dms:
+        temporary_view_name = final_o_view_name
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
+    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(tobytes(i_dms_name), tobytes(i_view_name), \
+                  tobytes(ref_dms_name), tobytes(ref_view_name), \
+                  tobytes(taxo_dms_name), tobytes(taxonomy_name), \
+                  tobytes(o_view_name), comments, 
+                  config['ecotag']['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)
+
+    #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, delete the temporary result view in the input DMS
+    if i_dms != o_dms:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    
+    i_dms.close()
+    
+    logger("info", "Done.")
+

python/obitools3/commands/export.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h

python/obitools3/commands/export.pyx

@@ -0,0 +1,69 @@
+#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.apps.optiongroups import addMinimalInputOption, \
+                                        addExportOutputOption
+
+import sys
+
+__title__="Export a view to a different file format"
+
+
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addExportOutputOption(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]
+            
+    # 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")
+   
+    # Initialize the progress bar
+    pb = ProgressBar(len(iview), config, seconde=5)
+    
+    i=0
+    for seq in iview :
+        pb(i)
+        try:
+            writer(seq)
+        except StopIteration:
+            break
+        i+=1
+
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
+    # TODO save command in input dms?
+    
+    output_object.close()
+    iview.close()
+    input[0].close()
+
+    logger("info", "Done.")

python/obitools3/commands/grep.cfiles

@@ -0,0 +1,103 @@
+../../../src/obi_lcs.h
+../../../src/obi_lcs.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/upperband.h
+../../../src/upperband.c
+../../../src/sse_banded_LCS_alignment.h
+../../../src/sse_banded_LCS_alignment.c
+../../../src/obiblob.h
+../../../src/obiblob.c
+../../../src/utils.h
+../../../src/utils.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/libjson/json_utils.h
+../../../src/libjson/json_utils.c
+../../../src/libjson/cJSON.h
+../../../src/libjson/cJSON.c
+../../../src/obiavl.h
+../../../src/obiavl.c
+../../../src/bloom.h
+../../../src/bloom.c
+../../../src/crc64.h
+../../../src/crc64.c
+../../../src/murmurhash2.h
+../../../src/murmurhash2.c
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obiblob_indexer.h
+../../../src/obiblob_indexer.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../src/hashtable.h
+../../../src/hashtable.c
+../../../src/linked_list.h
+../../../src/linked_list.c
+../../../src/obidmscolumn_array.h
+../../../src/obidmscolumn_array.c
+../../../src/obidmscolumn_blob.h
+../../../src/obidmscolumn_blob.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_qual.h
+../../../src/obidmscolumn_qual.c
+../../../src/obidmscolumn_seq.h
+../../../src/obidmscolumn_seq.c
+../../../src/obidmscolumn_str.h
+../../../src/obidmscolumn_str.c
+../../../src/array_indexer.h
+../../../src/array_indexer.c
+../../../src/char_str_indexer.h
+../../../src/char_str_indexer.c
+../../../src/dna_seq_indexer.h
+../../../src/dna_seq_indexer.c
+../../../src/encode.c
+../../../src/encode.h
+../../../src/uint8_indexer.c
+../../../src/uint8_indexer.h
+../../../src/build_reference_db.c
+../../../src/build_reference_db.h
+../../../src/kmer_similarity.c
+../../../src/kmer_similarity.h
+../../../src/obi_clean.c
+../../../src/obi_clean.h
+../../../src/obi_ecopcr.c
+../../../src/obi_ecopcr.h
+../../../src/obi_ecotag.c
+../../../src/obi_ecotag.h
+../../../src/obidms_taxonomy.c
+../../../src/obidms_taxonomy.h
+../../../src/obilittlebigman.c
+../../../src/obilittlebigman.h
+../../../src/_sse.h
+../../../src/obidebug.h
+../../../src/libecoPCR/libapat/CODES/dft_code.h
+../../../src/libecoPCR/libapat/CODES/dna_code.h
+../../../src/libecoPCR/libapat/CODES/prot_code.h
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/apat.h
+../../../src/libecoPCR/libapat/Gmach.h
+../../../src/libecoPCR/libapat/Gtypes.h
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/libapat/libstki.h
+../../../src/libecoPCR/libthermo/nnparams.h
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
+../../../src/libecoPCR/ecoPCR.h