Fixed stdout output

versions of python

.gitignore

@@ -1,13 +0,0 @@
-.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

@@ -1,17 +0,0 @@
-<?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

@@ -1,20 +0,0 @@
-<?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>

MANIFEST.in

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

README.md

@@ -1,9 +1,9 @@
 The `OBITools3`: A package for the management of analyses and data in DNA metabarcoding   
 ---------------------------------------------
 
+**Website: <https://metabarcoding.org/obitools3>**
 
-
-DNA metabarcoding offers new perspectives for biodiversity research [1]. This approach of ecosystem studies relies heavily on the use of Next-Generation Sequencing (NGS), and consequently requires the ability to to treat large volumes of data. The `OBITools` package  satisfies this requirement thanks to a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context [2] - <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.   
+DNA metabarcoding offers new perspectives for biodiversity research [1]. This approach of ecosystem studies relies heavily on the use of Next-Generation Sequencing (NGS), and consequently requires the ability to to treat large volumes of data. The `OBITools` package  satisfies this requirement thanks to a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context [2] - <https://metabarcoding.org/obitools>. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to setup tailored-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.   
 
 
 
@@ -23,18 +23,19 @@ DNA metabarcoding offers new perspectives for biodiversity research [1]. This ap
 
 
 
-**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`.    
+**Tools.** The `OBITools3` offer the same tools as the original `OBITools`, plus `ecoPCR` (*in silico* PCR) [4] and `Sumatra` (sequence alignment, not multithreaded yet) [5]. 
+Eventually, new versions of `ecoPrimers` (PCR primer design) [3], as well as `Sumaclust` (sequence alignment and clustering) [5] will be added, taking advantage of the database structure developed for the `OBITools3`.    
 
 
 
-**Implementation and disponibility.** The lower layers managing the DMS as well as all the compute-intensive functions are coded in `C99` for efficiency reasons. A `Cython` (<http://www.cython.org>) object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3.5`. The `OBITools3` are still in development, and the first functional versions are expected for autumn 2016.    
+**Implementation and disponibility.** The lower layers managing the DMS as well as all the compute-intensive functions are coded in `C99` for efficiency reasons. A `Cython` (<http://www.cython.org>) object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3`. The `OBITools3` are now being released, check the wiki for more information.
 
 
 
 **References.**
 
 1. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH: Environmental DNA. Mol Ecol 2012:1789–1793.
-2. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E: OBITools: a Unix-inspired software package for DNA metabarcoding. Mol Ecol Resour 2015:n/a–n/a.
+2. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E: OBITools: a Unix-inspired software package for DNA metabarcoding. Mol Ecol Resour, 2016: 176-182.
 3. Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E: ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res 2011, 39:e145.
 4. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, Taberlet P, Pompanon F: An in silico approach for the evaluation of DNA barcodes. BMC Genomics 2010, 11:434.
 5. Mercier C, Boyer F, Bonin A, Coissac E (2013) SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Available: <http://metabarcoding.org/sumatra> and <http://metabarcoding.org/sumaclust>

c-sandbox/obicount/Makefile

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

c-sandbox/obicount/obicount.c

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

doc/.gitignore

@@ -1,5 +0,0 @@
-/build/
-/doxygen/
-/build_dir.txt
-/.DS_Store
-/.gitignore

doc/Makefile

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

doc/conf.py

@@ -1,300 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# OBITools3 documentation build configuration file, created by
-# sphinx-quickstart on Mon May  4 14:36:57 2015.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-import sys
-import os
-import shlex
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.imgmath',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'breathe',
-]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'source/index'
-
-# General information about the project.
-project = u'OBITools3'
-copyright = u'2015, Céline Mercier, Eric Coissac, Frédéric Boyer'
-author = u'Céline Mercier, Eric Coissac, Frédéric Boyer'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '0.0'
-# The full version, including alpha/beta/rc tags.
-release = '0.0.0'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = []
-
-# The reST default role (used for this markup: `text`) to use for all
-# documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-# If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-html_theme = 'bizstyle'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#html_theme_options = {}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents.  If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-#html_logo = None
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# Add any extra paths that contain custom files (such as robots.txt or
-# .htaccess) here, relative to this directory. These files are copied
-# directly to the root of the documentation.
-#html_extra_path = []
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_domain_indices = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it.  The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Language to be used for generating the HTML full-text search index.
-# Sphinx supports the following languages:
-#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
-#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
-#html_search_language = 'en'
-
-# A dictionary with options for the search language support, empty by default.
-# Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
-
-# The name of a javascript file (relative to the configuration directory) that
-# implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'OBITools3doc'
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-  (master_doc, 'OBITools3.tex', u'OBITools3 Documentation',
-   u'Céline Mercier, Eric Coissac, Frédéric Boyer', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'obitools3', u'OBITools3 Documentation',
-     [author], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-  (master_doc, 'OBITools3', u'OBITools3 Documentation',
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-   'Miscellaneous'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-#texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
-
-#Breathe configuration
-sys.path.append( "breathe/" )
-breathe_projects = { "OBITools3": "doxygen/xml/" }
-breathe_default_project = "OBITools3"
-#breathe_projects_source = {
-#     "auto" : ( "../src", ["obidms.h", "obiavl.h"] )
-#     }

doc/source/DMS.rst

@@ -1,160 +0,0 @@
-*********************************************
-The OBItools3 Data Management System (OBIDMS)
-*********************************************
-
-A complete DNA metabarcoding experiment relies on several kinds of data.
-
-	- The sequence data resulting from the sequencing of the PCR products,
-	- The description of the samples including all their metadata,
-	- One or several reference databases used for the taxonomic annotation,
-	- One or several taxonomy databases.
-
-Up to now, each of these categories of data were stored in separate
-files, and nothing made it mandatory to keep them together.
-
-
-The `Data Management System` (DMS) of OBITools3 can be viewed like a basic 
-database system.
-
-
-OBIDMS UML
-==========
-
-.. image:: ./UML/OBIDMS_UML.png
-
-:download:`html version of the OBIDMS UML file <UML/ObiDMS_UML.class.violet.html>`
-
-
-An OBIDMS directory contains :
-  * one `OBIDMS history file <#obidms-history-files>`_
-  * OBIDMS column directories
-
-
-OBIDMS column directories
-=========================
-
-OBIDMS column directories contain :
-    * all the different versions of one OBIDMS column, under the form of different files (`OBIDMS column files <#obidms-column-files>`_)
-    * one `OBIDMS version file <#obidms-version-files>`_
-
-The directory name is the column attribute with the extension ``.obicol``.
-
-Example: ``count.obicol``
-
-
-OBIDMS column files
-===================
-
-Each OBIDMS column file contains :
-	* a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes
-	  on most systems) containing metadata
-	* Lines of data with the same `OBIType <types.html#obitypes>`_
-
-
-Header
-------
-
-The header of an OBIDMS column contains :
-
-	* Endian byte order
-	* Header size (PAGESIZE multiple)
-	* Number of lines of data
-	* Number of lines of data used
-	* `OBIType <types.html#obitypes>`_ (type of the data)
-	* Date of creation of the file
-	* Version of the OBIDMS column
-	* The column name
-	* Eventual comments
-
-
-Data
-----
-
-A line of data corresponds to a vector of elements. Each element is associated with an element name. 
-Elements names are stored in the header. The correspondance between an element and its name is done 
-using their order in the lists of elements and elements names.  This structure allows the storage of 
-dictionary-like data.
-
-Example: In the header, the attribute ``elements_names`` will be associated with the value ``"sample_1;
-sample_2;sample_3"``, and a line of data with the type ``OBInt_t`` will be stored as an ``OBInt_t`` vector 
-of size three e.g. ``5|8|4``.
-
-
-Mandatory columns
------------------
-
-Some columns must exist in an OBIDMS directory :
-    * sequence identifiers column (type ``OBIStr_t``)
-
-
-File name
----------
-
-Each file is named with the attribute associated to the data it contains, and the number of
-its version, separated by an ``@``, and with the extension ``.odc``.
-
-Example : ``count@3.odc``
-
-
-Modifications
--------------
-
-An OBIDMS column file can only be modified by the process that created it, and while its status is set to Open. 
-
-When a process wants to modify an OBIDMS column file that is closed, it must first clone it. Cloning creates a new version of the
-file that belongs to the process, i.e., only that process can modify that file, as long as its status is set to Open. Once the process
-has finished writing the new version of the column file, it sets the column file's status to Closed, and the file can never be modified
-again.
-
-That means that one column is stored in one file (if there is only one version)
-or more (if there are several versions), and that there is one file per version.
-
-All the versions of one column are stored in one directory.
-
-
-Versioning
-----------
-
-The first version of a column file is numbered 0, and each new version increments that
-number by 1.
-
-The number of the latest version of an OBIDMS column is stored in the `OBIDMS version file <#obidms-version-files>`_ of its directory.
-
-
-OBIDMS version files
-====================
-
-Each OBIDMS column is associated with an OBIDMS version file in its directory, that contains the number of the latest
-version of the column.
-
-File name
----------
-
-OBIDMS version files are named with the attribute associated to the data contained in the column, and
-have the extension ``.odv``.
-
-Example : ``count.odv``
-
-
-OBIDMS views
-============
-
-An OBIDMS view consists of a list of OBIDMS columns and lines. A view includes one version
-of each mandatory column. Only one version of each column is included. All the columns of
-one view contain the same number of lines in the same order.
-
-
-OBIDMS history file
-===================
-
-An OBIDMS history file consists of an ordered list of views and commands, those commands leading
-from one view to the next one.
-
-This history can be represented in the form of a ?? showing all the
-operations ever done in the OBIDMS directory and the views in between them :
-
-.. image:: ./images/history.png
-    :width: 150 px
-    :align: center
-
-

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doc/source/containers.rst

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

doc/source/data.rst

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

doc/source/elementary.rst

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

doc/source/guidelines.rst

@@ -1,131 +0,0 @@
-######################
-Programming guidelines
-######################
-
-
-***************
-Version control
-***************
-
-Version control is managed with `Git <http://git-scm.com/>`_. 
-Issue tracking and repository management are done using `GitLab <https://about.gitlab.com/>`_ 
-at http://git.metabarcoding.org/.
-
-
-Branching strategy
-==================
-
-
-Master branch
--------------
-
-The master branch should only contain functional scripts. 
-
-
-Topic branches
---------------
-
-Topic branches should correspond to development branches revolving around a topic corresponding 
-to the branch's name.
-
-
-Release branches
-----------------
-
-Release branches should start with duplicates of tags and be used to patch them. 
-
-
-Tags
-----
-
-Tags should never be committed to.
-
-
-Rebasing
---------
-
-Rebasing should be avoided on the distant server.
-
-
-Merging
--------
-
-Merging should never overwrite on a release branch or on a tag.
-
-
-Branching strategy diagram
---------------------------
-
-.. image:: ./images/version_control.png
-
-
-Issue tracking
-==============
-
-Issue tracking is done using `GitLab <https://about.gitlab.com/>`_ at http://git.metabarcoding.org/.
-Tickets should always be labeled with the branches for which they are relevant.
-
-
-*************
-Documentation
-*************
-
-C functions are documented in the header files for public functions, and in the source file for private functions.
-
-
-**************
-OBITools3 wiki
-**************
-
-The OBITools3 wiki is managed with GitLab.
-
-
-*********************
-Programming languages
-*********************
-
-C99 :
-	* All the low-level input/output functions (e.g. all the `OBIDMS <formats.html#the-obitools3-data-management-system-obidms>`_ functions)
-	* Computing-intensive code (e.g. alignment or pattern matching)
-	
-`Cython <cython.org>`_ :
-	* Object layer
-	* OBITools3 library
-
-`Python 3.5 <https://www.python.org/>`_ :
-	* Top layer code (scripts)	
-	
-For the documentation, `Sphinx <http://sphinx-doc.org/>`_ should be used for both the original 
-documentation and for the generation of documentation from the python code. `Doxygen <http://www.stack.nl/~dimitri/doxygen/>`_ 
-should be used for the generation of documentation from the C code, which should be then integrated 
-in the Sphinx documentation using `Breathe <https://breathe.readthedocs.org/en/latest/>`_.
-
-
-******************
-Naming conventions
-******************
-
-Struct, Enum:                                   ``Title_case``
-
-Enum members, macros, constants:                ``ALL_CAPS``
-
-Functions, local variables:                     ``lower_case``
-
-Public functions:                               ``obi_lower_case``
-
-Functions that shouldn't be called directly:    ``_lower_case`` (``_`` prefix)
-
-Global variables:                                ``g_lower_case`` (``g_`` prefix)
-
-Pointers:                                        ``pointer_ptr`` (``_ptr`` suffix)
-
-.. note::
-    Underscores are used to delimit 'words'.
-
-
-*****************
-Programming rules
-*****************
-
-    * 
-

doc/source/index.rst

@@ -1,21 +0,0 @@
-.. OBITools3 documentation master file, created by
-   sphinx-quickstart on Mon May  4 14:36:57 2015.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-OBITools3 documentation
-==========================
-
-.. toctree::
-   :maxdepth: 2
-
-   Programming guidelines <guidelines>
-   Data structures <data>
-   Code documentation <code_doc/codedoc>
-
-Indices and tables
-------------------
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

doc/source/specialvalues.rst

@@ -1,55 +0,0 @@
-==============
-Special values
-==============
-
-
-NA values
-=========
-
-All OBITypes have an associated NA (Not Available) value. 
-NA values are implemented by specifying an explicit NA value for each type, 
-corresponding to the R standards as much as possible:
-
-* For the type ``OBIInt_t``, the NA value is ``INT_MIN``.
-
-* For the type ``OBIBool_t``, the NA value is ``2``.
-
-* For the type ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``SIZE_MAX``.
-
-* For the type ``OBIChar_t``: the NA value is ``\0``.
-
-* For the type ``OBIFloat_t``::
-
-    typedef union
-    {
-        double value;
-        unsigned int word[2];
-    } ieee_double;
-    
-    static double NA_value(void)
-    {
-        volatile ieee_double x;
-        x.word[hw] = 0x7ff00000;
-        x.word[lw] = 1954;
-        return x.value;
-    }
-
-
-Minimum and maximum values for ``OBIInt_t``
-===========================================
-
-* Maximum value : ``INT_MAX``
-* Minimum value : ``INT_MIN(-1?)``
-
-
-Infinity values for the type ``OBIFloat_t``
-===========================================
-
-* Positive infinity : ``INFINITY`` (should be defined in ``<math.h>``)
-* Negative infinity : ``-INFINITY``
-
-
-NaN value for the type ``OBIFloat_t``
-=====================================
-
-* NaN (Not a Number) value : ``NAN`` (should be defined in ``<math.h>`` but probably needs to be tested)

doc/source/types.rst

@@ -1,21 +0,0 @@
-********
-OBITypes
-********
-
-    
-.. image:: ./UML/OBITypes_UML.png
-
-:download:`html version of the OBITypes UML file <UML/OBITypes_UML.class.violet.html>`
-
-
-.. image:: ./UML/Obicolumn_classes_UML.png
-
-:download:`html version of the OBIDMS classes UML file <UML/Obicolumn_classes_UML.class.violet.html>`
-
-
-.. toctree::
-   :maxdepth: 2
-
-   The elementary types <elementary>
-   The containers <containers>
-   Special values <specialvalues>

doc/sphinx/.gitignore

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

obi_completion_script.bash

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

python/.gitignore

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

python/obitools3/.gitignore

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

python/obitools3/apps/arguments.cfiles

@@ -1,110 +0,0 @@
-../../../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.pyx

@@ -33,10 +33,6 @@ cpdef buildArgumentParser(str configname,
                                        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',

python/obitools3/apps/command.cfiles

@@ -1,110 +0,0 @@
-../../../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.cfiles

@@ -1,110 +0,0 @@
-../../../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.pyx

@@ -13,7 +13,7 @@ from .logging   cimport getLogger
 from .arguments cimport buildArgumentParser
 
 from ..version import version
-from _curses import version
+
 
 cdef dict __default_config__ = {}
 

python/obitools3/apps/logging.cfiles

@@ -1,110 +0,0 @@
-../../../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/optiongroups/__init__.py

@@ -1,3 +1,9 @@
+import codecs
+
+def unescaped_str(arg_str):
+    return arg_str.encode('latin-1', 'backslashreplace').decode('unicode-escape')
+
+
 def __addInputOption(optionManager):
     
     optionManager.add_argument(
@@ -39,6 +45,30 @@ def __addImportInputOption(optionManager):
                      const=b'fastq',
                      help="Input file is in fastq format")
 
+    group.add_argument('--silva-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'silva',
+                     help="Input file is in SILVA fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
+    group.add_argument('--rdp-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'rdp',
+                     help="Input file is in RDP training set fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
+    group.add_argument('--unite-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'unite',
+                     help="Input file is in UNITE fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
+    group.add_argument('--sintax-input',
+                     action="store_const", dest="obi:inputformat",
+                     default=None,
+                     const=b'sintax',
+                     help="Input file is in SINTAX fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
+
     group.add_argument('--embl-input',
                      action="store_const", dest="obi:inputformat",
                      default=None,
@@ -55,7 +85,7 @@ def __addImportInputOption(optionManager):
                      action="store_const", dest="obi:inputformat",
                      default=None,
                      const=b'ngsfilter',
-                     help="Input file is an ngsfilter file")
+                     help="Input file is an ngsfilter file. If not using tags, use ':' or 'None:None' or '-:-' or any combination")
 
     group.add_argument('--ecopcr-result-input',
                      action="store_const", dest="obi:inputformat",
@@ -115,20 +145,26 @@ def __addImportInputOption(optionManager):
                      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")
+def __addTabularOption(optionManager):
+    group = optionManager.add_argument_group("Input and output format options for tabular files")
+
+    group.add_argument('--no-header',
+                     action="store_false", dest="obi:header",
+                     default=True,
+                     help="Don't print the header (first line with column names")
 
     group.add_argument('--sep',
                      action="store", dest="obi:sep",
-                     default=None,
-                     type=str,
+                     default="\t",
+                     type=unescaped_str,
                      help="Column separator")
+
+
+def __addTabularInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for tabular files")
+    
+    __addTabularOption(optionManager)
     
     group.add_argument('--dec',
                      action="store", dest="obi:dec",
@@ -153,6 +189,16 @@ def __addTabularInputOption(optionManager):
                      help="Lines starting by this char are considered as comment")
 
 
+def __addTabularOutputOption(optionManager):
+    group = optionManager.add_argument_group("Output format options for tabular files")
+    
+    __addTabularOption(optionManager)
+
+    group.add_argument('--na-int-stay-na',
+                     action="store_false", dest="obi:na_int_to_0",
+                     help="NA (Non available) integer values should be exported as NA in tabular output (default: they are converted to 0 for tabular output).") # TODO
+
+
 def __addTaxdumpInputOption(optionManager):  # TODO maybe not the best way to do it
     group = optionManager.add_argument_group("Input format options for taxdump")
 
@@ -186,6 +232,10 @@ def addTabularInputOption(optionManager):
     __addTabularInputOption(optionManager)
 
 
+def addTabularOutputOption(optionManager):
+    __addTabularOutputOption(optionManager)
+
+
 def addTaxonomyOption(optionManager):
     __addTaxonomyOption(optionManager)
 
@@ -198,6 +248,7 @@ def addAllInputOption(optionManager):
     __addInputOption(optionManager)
     __addImportInputOption(optionManager)
     __addTabularInputOption(optionManager)
+    __addTabularOutputOption(optionManager)
     __addTaxonomyOption(optionManager)
     __addTaxdumpInputOption(optionManager)    
 
@@ -205,7 +256,7 @@ def addAllInputOption(optionManager):
 def __addOutputOption(optionManager):
     
     optionManager.add_argument(
-                    dest='obi:outputURI',  
+                    dest='obi:outputURI',
                     metavar='OUTPUT', 
                     help='Data destination URI')
 
@@ -216,12 +267,15 @@ def __addDMSOutputOption(optionManager):
     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")
+                 help="Don't create an output DMS if it does not already exist")
 
+
+def __addEltLimitOption(optionManager):
+    group = optionManager.add_argument_group("Option to limit the number of elements per line in columns")
     group.add_argument('--max-elts',
                  action="store", dest="obi:maxelts",
                  metavar='<N>',
-                 default=1000,
+                 default=1000000,
                  type=int,
                  help="Maximum number of elements per line in a column "
                       "(e.g. the number of different keys in a dictionary-type "
@@ -232,6 +286,11 @@ def __addDMSOutputOption(optionManager):
 def __addExportOutputOption(optionManager):
     group = optionManager.add_argument_group("Output format options for exported files")
 
+    group.add_argument('-o',
+                    dest='obi:outputURI',
+                    metavar='OUTPUT', 
+                    help='Data destination URI')
+
     group.add_argument('--fasta-output',
                      action="store_const", dest="obi:outputformat",
                      default=None,
@@ -244,6 +303,41 @@ def __addExportOutputOption(optionManager):
                      const=b'fastq',
                      help="Output file is in fastq format")
 
+    group.add_argument('--tab-output',
+                     action="store_const", dest="obi:outputformat",
+                     default=None,
+                     const=b'tabular',
+                     help="Output file is in tabular format")
+
+    group.add_argument('--metabaR-output',
+                     action="store_const", dest="obi:outputformat",
+                     default=None,
+                     const=b'metabaR',
+                     help="Export the files needed by the obifiles_to_metabarlist function of the metabaR package")
+
+    group.add_argument('--metabaR-prefix',
+                     action="store", dest="obi:metabarprefix",
+                     type=str,
+                     help="Prefix for the files when using --metabaR-output option")
+
+    group.add_argument('--metabaR-ngsfilter',
+                     action="store", dest="obi:metabarngsfilter",
+                     type=str,
+                     default=None,
+                     help="URI to the ngsfilter view when using --metabaR-output option (if not provided, it is not exported)")
+
+    group.add_argument('--metabaR-samples',
+                     action="store", dest="obi:metabarsamples",
+                     type=str,
+                     default=None,
+                     help="URI to the sample metadata view when using --metabaR-output option (if not provided, it is built as just a list of the sample names)")
+
+    group.add_argument('--only-keys',
+                       action="append", dest="obi:only_keys",
+                       type=str,
+                       default=[],
+                       help="Only export the given keys (columns).")
+
     group.add_argument('--print-na',
                      action="store_true", dest="obi:printna",
                      default=False,
@@ -256,17 +350,40 @@ def __addExportOutputOption(optionManager):
                      help="String associated with Non Available (NA) values in the output")
 
 
+def __addNoProgressBarOption(optionManager):
+    group = optionManager.add_argument_group("Option to deactivate the display of the progress bar")
+
+    group.add_argument('--no-progress-bar',
+                     action="store_true", dest="obi:noprogressbar",
+                     default=False,
+                     help="Do not display progress bar")
+
+
 def addMinimalOutputOption(optionManager):
     __addOutputOption(optionManager)
     __addDMSOutputOption(optionManager)
 
+
+def addTabularOutputOption(optionManager):
+    __addTabularOption(optionManager)
+
+
 def addExportOutputOption(optionManager):
-    __addOutputOption(optionManager)
     __addExportOutputOption(optionManager)
+    __addTabularOutputOption(optionManager)
 
 
 def addAllOutputOption(optionManager):
     __addOutputOption(optionManager)
     __addDMSOutputOption(optionManager)
     __addExportOutputOption(optionManager)
+    __addTabularOutputOption(optionManager)
 
+
+def addNoProgressBarOption(optionManager):
+    __addNoProgressBarOption(optionManager)
+    
+def addEltLimitOption(optionManager):
+    __addEltLimitOption(optionManager)
+    
+    

python/obitools3/apps/progress.cfiles

@@ -1,110 +0,0 @@
-../../../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.pyx

@@ -30,12 +30,12 @@ cdef class ProgressBar:
                  off_t maxi,
                  dict  config={},
                  str head="",
-                 double seconde=0.1,
+                 double seconds=5,
                  cut=False):
         
         self.starttime = self.clock()
         self.lasttime  = self.starttime
-        self.tickcount = <clock_t> (seconde * CLOCKS_PER_SEC)
+        self.tickcount = <clock_t> (seconds * CLOCKS_PER_SEC)
         self.freq      = 1
         self.cycle     = 0
         self.arrow     = 0

python/obitools3/apps/temp.cfiles

@@ -1,110 +0,0 @@
-../../../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/.gitignore

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

python/obitools3/commands/addtaxids.pyx

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

python/obitools3/commands/align.cfiles

@@ -1,103 +0,0 @@
-../../../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.pyx

@@ -4,7 +4,7 @@ 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.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
@@ -12,17 +12,21 @@ from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \
                                             obi_lcs_align_two_columns
 
+from io import BufferedWriter
+from cpython.exc cimport PyErr_CheckSignals
+
 import time
 import sys
 
 
-__title__="Aligns one sequence column with itself or two sequence columns"
+__title__="Align one sequence column with itself or two sequence columns"
 
 
 def addOptions(parser):
    
    addMinimalInputOption(parser)
    addMinimalOutputOption(parser)
+   addNoProgressBarOption(parser)
 
    group=parser.add_argument_group('obi align specific options')
 
@@ -154,7 +158,7 @@ def run(config):
     i_view_name = i_uri.split(b"/")[0]
     i_column_name = b""
     i_element_name = b""
-    if len(i_uri.split(b"/")) == 2:
+    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]
@@ -177,7 +181,7 @@ def run(config):
         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:
+        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]
@@ -201,20 +205,20 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     o_dms_name = o_dms.name 
     final_o_view_name = output[1]
+    o_view_name = final_o_view_name
 
-    # If the input and output DMS are not the same, align creating a temporary view in the input dms that will be exported to 
+    # If stdout output or the input and output DMS are not the same, align creating a temporary view in the input dms that will be exported to 
     # the right DMS and deleted in the other afterwards.
-    if i_dms != o_dms:
-        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))
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
             i+=1
-        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:])
@@ -229,7 +233,7 @@ def run(config):
     
     # Call cython alignment function
       # Using default ID columns of the view. TODO discuss adding option
-    align_columns(i_dms_name,  \
+    align_columns(i_dms.name_with_full_path,  \
                   i_view_name,  \
                   o_view_name,  \
                   input_view_2_n   = i_view_name_2,  \
@@ -263,12 +267,19 @@ def run(config):
         View.delete_view(i_dms, i_view_name_2)
         i_dms_2.close()
 
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     # If the input and the output DMS are different, delete the temporary result view in the input DMS
-    if i_dms != o_dms:
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    i_dms.close(force=True)
     
     logger("info", "Done.")
   

python/obitools3/commands/alignpairedend.cfiles

@@ -1,103 +0,0 @@
-../../../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.pyx

@@ -2,12 +2,11 @@
 
 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.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.libalign._qsassemble import QSolexaReverseAssemble
@@ -15,13 +14,16 @@ 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
+from obitools3.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
+from obitools3.utils cimport str2bytes
 
+from io import BufferedWriter
 import sys
 import os
 
+from cpython.exc cimport PyErr_CheckSignals
 
-__title__="Aligns paired-ended reads"
+__title__="Align paired-ended reads"
 
 
 
@@ -29,6 +31,7 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
  
     group = parser.add_argument_group('obi alignpairedend specific options')
 
@@ -39,24 +42,25 @@ def addOptions(parser):
                      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('--score-min',
+#                      action="store", dest="alignpairedend:smin",
+#                      metavar="#.###",
+#                      default=None,
+#                      type=float,
+#                      help="Minimum score for keeping alignments. " 
+#                           "(for kmer alignment) The score is an approximation of the number of nucleotides matching in the overlap of the alignment.")
 
-    group.add_argument('-A', '--true-ali',
-                       action="store_true", dest="alignpairedend:trueali",
-                       default=False,
-                       help="Performs gap free end alignment of sequences instead of using kmers to compute alignments (slower).")
+#     group.add_argument('-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)")
+                       help="K-mer size for kmer comparisons, between 1 and 4 (default: 3)")
 
 
 la = QSolexaReverseAssemble()
@@ -96,12 +100,13 @@ def alignmentIterator(entries, aligner):
         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 = Nuc_Seq(seqF.id, seqF[REVERSE_SEQUENCE_COLUMN], quality=seqF[REVERSE_QUALITY_COLUMN])
             seqR.index = i
         
         ali = aligner(seqF, seqR)
@@ -169,81 +174,120 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
 
-    view = output[1]
+    output_0 = output[0]
+    o_dms = output[0]
     
-    Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)   #TODO output URI quality option?
-
-    if 'smin' in config['alignpairedend']:
-        smin = config['alignpairedend']['smin']
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        i_dms = forward.dms   # using any dms
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view = View_NUC_SEQS.new(o_dms, o_view_name, quality=True)
     else:
-        smin = 0
+        o_view = output[1]
+        Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL)
 
     # 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'])
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(entries_len, config)
+    else:
+        pb = None
+         
+    #if config['alignpairedend']['trueali']:
+    #    kmer_ali = False
+    #    aligner = buildAlignment
+    #else :
+    kmer_ali = True
+    if type(entries) == list:
+        forward = entries[0]
+        reverse = entries[1]
+        if len(forward) == 0 or len(reverse) == 0:
+            aligner = None
         else:
-            aligner = Kmer_similarity(entries, column2=entries[REVERSE_SEQ_COLUMN_NAME], qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], kmer_size=config['alignpairedend']['kmersize'])
+            aligner = Kmer_similarity(forward, \
+                                      view2=reverse, \
+                                      kmer_size=config['alignpairedend']['kmersize'], \
+                                      reversed_column=None)
+    else:
+        if len(entries) == 0:
+            aligner = None
+        else:
+            aligner = Kmer_similarity(entries, \
+                                      column2=entries[REVERSE_SEQUENCE_COLUMN], \
+                                      qual_column2=entries[REVERSE_QUALITY_COLUMN], \
+                                      kmer_size=config['alignpairedend']['kmersize'], \
+                                      reversed_column=entries[b'reversed'])  # column created by the ngsfilter tool
         
     ba = alignmentIterator(entries, aligner)
-
+    
     i = 0
     for ali in ba:
         
-        pb(i)
+        if pb is not None:
+            pb(i)
         
-        consensus = view[i]
+        PyErr_CheckSignals()
+
+        consensus = o_view[i]
         
+        if two_views:
+            consensus[b"R1_parent"] = forward[i].id
+            consensus[b"R2_parent"] = reverse[i].id
+               
         if not two_views:
             seqF = entries[i]
         else:
             seqF = forward[i]
-                
-        if 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:
+                        
+        if ali.overlap_len > 0 :
             buildConsensus(ali, consensus, seqF)
-                
+        else:
+            if not two_views:
+                seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQUENCE_COLUMN], quality = seqF[REVERSE_QUALITY_COLUMN])
+            else:
+                seqR = reverse[i]
+            buildJoinedSequence(ali, seqR, consensus, forward=seqF)
+                   
         if kmer_ali :
             ali.free()
     
         i+=1
 
-    pb(i, force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
 
-    if kmer_ali :
+    if kmer_ali and aligner is not None:
         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)
+    o_view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(view), file=sys.stderr)
-    
-    input[0].close()
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If stdout output, delete the temporary imported view used to create the final file
+    if type(output_0)==BufferedWriter:
+        View_NUC_SEQS.delete_view(o_dms, o_view_name)
+        output_0.close()
+
+    # Close all DMS
+    input[0].close(force=True)
     if two_views:
-        rinput[0].close()
-    output[0].close()
+        rinput[0].close(force=True)
+    o_dms.close(force=True)
 
     logger("info", "Done.")
     

python/obitools3/commands/annotate.cfiles

@@ -1,103 +0,0 @@
-../../../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

@@ -4,21 +4,27 @@ 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.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from functools import reduce
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
+from io import BufferedWriter
 from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
                                         ID_COLUMN, \
                                         DEFINITION_COLUMN, \
                                         QUALITY_COLUMN, \
-                                        COUNT_COLUMN
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN
+from obitools3.dms.capi.obitypes cimport OBI_STR
+from obitools3.dms.column.column cimport Column
 
 import time
 import math 
 import sys
 
+from cpython.exc cimport PyErr_CheckSignals
+
  
 __title__="Annotate views with new tags and edit existing annotations"
 
@@ -31,6 +37,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi annotate specific options')
  
@@ -173,8 +180,8 @@ def sequenceTaggerGenerator(config, taxo=None):
             counter[0]+=1
                             
         for rank in annoteRank:
-            if 'taxid' in seq:
-                taxid = seq['taxid']
+            if TAXID_COLUMN in seq:
+                taxid = seq[TAXID_COLUMN]
                 if taxid is not None:
                     rtaxid = taxo.get_taxon_at_rank(taxid, rank)
                     if rtaxid is not None:
@@ -182,64 +189,58 @@ def sequenceTaggerGenerator(config, taxo=None):
                     else:
                         scn=None
                     seq[rank]=rtaxid
+                    if "%s_name"%rank not in seq.view:
+                        Column.new_column(seq.view, "%s_name"%rank, OBI_STR)
                     seq["%s_name"%rank]=scn
              
         if add_rank:
             seq['seq_rank']=counter[0]
     
         for i,v in toSet:
-            #try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}
-            val = eval(v, environ, seq)
-            #except Exception,e:       # TODO discuss usefulness of this
-            #    if options.onlyValid:
-            #        raise e
-            #    val = v
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}
+                val = eval(v, environ, seq)
+            except Exception:       # set string if not a valid expression
+                val = v
             seq[i]=val
 
         if length:
             seq['seq_length']=len(seq)
 
         if newId is not None:
-#            try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
-            val = eval(newId, environ, seq)
-#            except Exception,e:
-#                if options.onlyValid:
-#                    raise e
-#                val = newId
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newId, environ, seq)
+            except Exception:      # set string if not a valid expression
+                val = newId
             seq.id=val
 
         if newDef is not None:
-#            try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
-            val = eval(newDef, environ, seq)
-#            except Exception,e:
-#                if options.onlyValid:
-#                    raise e
-#                val = newDef
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newDef, environ, seq)
+            except Exception:    # set string if not a valid expression
+                val = newDef
             seq.definition=val
-#             
+             
         if newSeq is not None:
-#            try:
-            if taxo is not None:
-                environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
-            else:
-                environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
-            val = eval(newSeq, environ, seq)
-#            except Exception,e:
-#                if options.onlyValid:
-#                    raise e
-#                val = newSeq
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                val = eval(newSeq, environ, seq)
+            except Exception:    # set string if not a valid expression
+                val = newSeq
             seq.seq=val
             if 'seq_length' in seq:
                 seq['seq_length']=len(seq)
@@ -249,15 +250,14 @@ def sequenceTaggerGenerator(config, taxo=None):
                 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
+            try:
+                if taxo is not None:
+                    environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
+                else:
+                    environ = {'sequence':seq, 'counter':counter[0], 'math':math}     
+                eval(run, environ, seq)
+            except Exception,e:
+                raise e
 
     return sequenceTagger
 
@@ -284,8 +284,19 @@ def run(config):
     if output is None:
         raise Exception("Could not create output view")
     o_dms = output[0]
+    output_0 = output[0]
     o_view_name = output[1]
-    
+
+    # stdout output: create temporary view
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        i=0
+        o_view_name = b"temp"
+        while o_view_name in i_dms: # Making sure view name is unique in output DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        imported_view_name = o_view_name
+
     # If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
     # (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
     if i_dms != o_dms:
@@ -296,7 +307,7 @@ def run(config):
             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:
@@ -306,14 +317,17 @@ def run(config):
     # 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:
+        if taxo_uri is None or taxo_uri[2] == bytes:
             raise Exception("Couldn't open taxonomy")
         taxo = taxo_uri[1]
     else :
         taxo = None
 
     # Initialize the progress bar
-    pb = ProgressBar(len(o_view), config, seconde=5)
+    if config['obi']['noprogressbar'] == False:
+        pb = ProgressBar(len(o_view), config)
+    else:
+        pb = None
 
     try:
 
@@ -351,14 +365,17 @@ def run(config):
         # Editions at line level
         sequenceTagger = sequenceTaggerGenerator(config, taxo=taxo)
         for i in range(len(o_view)):
-            pb(i)
+            PyErr_CheckSignals()
+            if pb is not None:
+                pb(i)
             sequenceTagger(o_view[i])
 
     except Exception, e:
         raise RollbackException("obi annotate error, rollbacking view: "+str(e), o_view)
 
-    pb(i, force=True)
-    print("", file=sys.stderr)
+    if pb is not None:
+        pb(i, force=True)
+        print("", file=sys.stderr)
     
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
@@ -368,15 +385,21 @@ def run(config):
         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)
+    o_dms.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:
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(o_dms, imported_view_name)
-        o_dms.close()
-    i_dms.close()
+        o_dms.close(force=True)
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/build_ref_db.cfiles

@@ -1,103 +0,0 @@
-../../../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

@@ -4,17 +4,19 @@ 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.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
+from io import BufferedWriter
 import sys
+from cpython.exc cimport PyErr_CheckSignals
 
 
-__title__="Tag a set of sequences for PCR and sequencing errors identification"
+__title__="Build a reference database for ecotag"
 
 
 def addOptions(parser):
@@ -22,16 +24,16 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
  
     group = parser.add_argument_group('obi build_ref_db specific options')
 
     group.add_argument('--threshold','-t',
                       action="store", dest="build_ref_db:threshold",
                       metavar='<THRESHOLD>',
-                      default=0.0,
+                      default=0.99,
                       type=float,
-                      help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.00"
-                           " (no threshold).")
+                      help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.99.")
 
 
 def run(config):
@@ -56,17 +58,20 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     final_o_view_name = output[1]
     
-    # If the input and output DMS are not the same, build the database creating a temporary view that will be exported to 
+    # If stdout output or the input and output DMS are not the same, build the database creating a temporary view that will be exported to 
     # the right DMS and deleted in the other afterwards.
-    if i_dms != o_dms:
-        temporary_view_name = final_o_view_name
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
         while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
             i+=1
         o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
     else:
         o_view_name = final_o_view_name
 
@@ -80,26 +85,33 @@ def run(config):
     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:
+    
+    if build_reference_db(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
         raise Exception("Error building a reference database")
     
     # If the input and output DMS are not the same, export result view to output DMS
     if i_dms != o_dms:
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-    
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary result view in the input DMS
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    i_dms.close(force=True)
 
     logger("info", "Done.")
     

python/obitools3/commands/cat.pyx

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

python/obitools3/commands/clean.cfiles

@@ -1,103 +0,0 @@
-../../../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

@@ -4,13 +4,14 @@ 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.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
+from io import BufferedWriter
 import sys
 
 
@@ -21,7 +22,8 @@ def addOptions(parser):
 
     addMinimalInputOption(parser)
     addMinimalOutputOption(parser)
- 
+    addNoProgressBarOption(parser)
+    
     group = parser.add_argument_group('obi clean specific options')
 
     group.add_argument('--distance', '-d',
@@ -36,8 +38,7 @@ def addOptions(parser):
                        dest="clean:sample-tag-name",
                        metavar="<SAMPLE TAG NAME>",
                        type=str,
-                       default="merged_sample",
-                       help="Name of the tag where sample counts are kept.")
+                       help="Name of the tag where merged sample count informations are kept (typically generated by obi uniq, usually MERGED_sample, default: None).")
     
     group.add_argument('--ratio', '-r',
                        action="store", dest="clean:ratio",
@@ -53,11 +54,18 @@ def addOptions(parser):
                        default=False,
                        help="Only sequences labeled as heads are kept in the output. Default: False")
 
-    group.add_argument('--cluster-tags', '-C',
-                       action="store_true", 
-                       dest="clean:cluster-tags",
-                       default=False,
-                       help="Adds tags for each sequence giving its cluster's head and weight for each sample.")
+#    group.add_argument('--cluster-tags', '-C',
+#                       action="store_true", 
+#                       dest="clean:cluster-tags",
+#                       default=False,
+#                       help="Adds tags for each sequence giving its cluster's head and weight for each sample.")
+
+    group.add_argument('--thread-count','-p',   # TODO should probably be in a specific option group
+                       action="store", dest="clean:thread-count",
+                       metavar='<THREAD COUNT>',
+                       default=-1,
+                       type=int,
+                       help="Number of threads to use for the computation. Default: the maximum available.")
 
 
 def run(config):
@@ -82,17 +90,20 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     final_o_view_name = output[1]
     
-    # If the input and output DMS are not the same, run obiclean creating a temporary view that will be exported to 
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported to 
     # the right DMS and deleted in the other afterwards.
-    if i_dms != o_dms:
-        temporary_view_name = final_o_view_name
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
         while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
             i+=1
         o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
     else:
         o_view_name = final_o_view_name
         
@@ -100,25 +111,36 @@ def run(config):
     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:
+    if 'sample-tag-name' not in config['clean']:
+        config['clean']['sample-tag-name'] = ""
+        
+    if obi_clean(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
+              config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], config['clean']['thread-count']) < 0:
         raise Exception("Error running obiclean")
     
     # If the input and output DMS are not the same, export result view to output DMS
     if i_dms != o_dms:
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
-    
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary result view in the input DMS
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    i_dms.close(force=True)
 
-    logger("info", "Done.")
+    logger("info", "Done.")
+    

python/obitools3/commands/clean_dms.pyx

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

python/obitools3/commands/count.cfiles

@@ -1,103 +0,0 @@
-../../../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

@@ -7,8 +7,10 @@ from obitools3.dms import DMS
 from obitools3.apps.optiongroups import addMinimalInputOption
 from obitools3.dms.capi.obiview cimport COUNT_COLUMN
 
+from cpython.exc cimport PyErr_CheckSignals
 
-__title__="Counts sequence records"
+
+__title__="Count sequence records"
 
  
 def addOptions(parser):
@@ -20,13 +22,19 @@ def addOptions(parser):
     group.add_argument('-s','--sequence',
                         action="store_true", dest="count:sequence",
                         default=False,
-                        help="Prints only the number of sequence records.")
+                        help="Prints only the number of sequence records (much faster, default: False).")
  
     group.add_argument('-a','--all',
                         action="store_true", dest="count:all",
                         default=False,
                         help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False).")
 
+    group.add_argument('-c','--count-tag',
+                        action="store", dest="count:countcol",
+                        default='COUNT',
+                        type=str,
+                        help="Name of the tag/column associated with the count information (default: COUNT).")
+
     
 def run(config):
     
@@ -39,17 +47,22 @@ def run(config):
     if input is None:
         raise Exception("Could not read input")
     entries = input[1]
-
+    
+    countcol = config['count']['countcol'] 
+    
     count1 = len(entries)
     count2 = 0
     
-    if COUNT_COLUMN in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
+    if countcol in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
         for e in entries:
-            count2+=e[COUNT_COLUMN]
+            PyErr_CheckSignals()
+            count2+=e[countcol]
 
-    if COUNT_COLUMN in entries and (config['count']['sequence'] == config['count']['all']):
+    if countcol in entries and (config['count']['sequence'] == config['count']['all']):
         print(count1,count2)
-    elif COUNT_COLUMN in entries and config['count']['all']:
+    elif countcol in entries and config['count']['all']:
         print(count2)
     else:
         print(count1)
+    
+    input[0].close(force=True)

python/obitools3/commands/ecopcr.cfiles

@@ -1,103 +0,0 @@
-../../../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

@@ -5,10 +5,10 @@ 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.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addTaxonomyOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
-from obitools3.utils cimport tobytes
+from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.view import View
 
@@ -16,6 +16,7 @@ from libc.stdlib  cimport malloc, free
 from libc.stdint  cimport int32_t
 
 import sys
+from io import BufferedWriter
 
 
 __title__="in silico PCR"
@@ -27,6 +28,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
  
     group = parser.add_argument_group('obi ecopcr specific options')
@@ -35,13 +37,15 @@ def addOptions(parser):
                        action="store", dest="ecopcr:primer1",
                        metavar='<PRIMER>',
                        type=str,
-                       help="Forward primer.")
+                       required=True,
+                       help="Forward primer, length must be less than or equal to 32")
 
     group.add_argument('--primer2', '-R',
                        action="store", dest="ecopcr:primer2",
                        metavar='<PRIMER>',
                        type=str,
-                       help="Reverse primer.")
+                       required=True,
+                       help="Reverse primer, length must be less than or equal to 32")
 
     group.add_argument('--error', '-e',
                        action="store", dest="ecopcr:error",
@@ -107,14 +111,20 @@ def addOptions(parser):
                        help="Defines the method used for estimating the Tm (melting temperature) between the primers and their corresponding "
                             "target sequences. SANTALUCIA: 1, or OWCZARZY: 2. Default: 1.")
 
+    group.add_argument('--keep-primers', '-p',
+                       action="store_true", 
+                       dest="ecopcr:keep-primers",
+                       default=False,
+                       help="Whether to keep the primers attached to the output sequences (default: the primers are cut out).")
+
     group.add_argument('--keep-nucs', '-D',
                        action="store", 
                        dest="ecopcr:keep-nucs",
-                       metavar="<INTEGER>",
+                       metavar="<N>",
                        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).")
+                       help="Keeps N nucleotides on each side of the in silico amplified sequences, "
+                            "not including the primers (implying that primers are automatically kept if N > 0).")
 
     group.add_argument('--kingdom-mode', '-k',
                        action="store_true", 
@@ -161,11 +171,28 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     o_dms_name = output[0].name
     o_view_name = output[1]
 
+    # Open the taxonomy DMS
+    taxdms = open_uri(config['obi']['taxoURI'],
+                     dms_only=True)
+    if taxdms is None:
+        raise Exception("Could not open taxonomy DMS")
+    tax_dms = taxdms[0]
+    tax_dms_name = taxdms[0].name
+    
     # Read taxonomy name    
     taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
+
+    # If stdout output create a temporary view in the input dms that will be deleted afterwards.
+    if type(output_0)==BufferedWriter:
+        o_dms = i_dms
+        o_view_name = b"temp"
+        while o_view_name in i_dms:   # Making sure view name is unique in input DMS
+            o_view_name = o_view_name+b"_"+str2bytes(str(i))
+            i+=1
     
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
@@ -178,14 +205,15 @@ def run(config):
 
     # 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, \
+    if obi_ecopcr(i_dms.name_with_full_path, tobytes(i_view_name), 
+                  tax_dms.name_with_full_path, tobytes(taxonomy_name), \
+                  o_dms.name_with_full_path, tobytes(o_view_name), comments, \
                   tobytes(config['ecopcr']['primer1']), tobytes(config['ecopcr']['primer2']), \
                   config['ecopcr']['error'], \
                   config['ecopcr']['min-length'], config['ecopcr']['max-length'], \
                   restrict_to_taxids_p, ignore_taxids_p, \
                   config['ecopcr']['circular'], config['ecopcr']['salt-concentration'], config['ecopcr']['salt-correction-method'], \
-                  config['ecopcr']['keep-nucs'], config['ecopcr']['kingdom-mode']) < 0:
+                  config['ecopcr']['keep-nucs'], config['ecopcr']['keep-primers'], config['ecopcr']['kingdom-mode']) < 0:
         raise Exception("Error running ecopcr")
 
     # Save command config in DMS comments
@@ -193,10 +221,22 @@ def run(config):
 
     free(restrict_to_taxids_p)
     free(ignore_taxids_p)
-    
+
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[o_view_name]), file=sys.stderr)
 
-    o_dms.close()
+    # If stdout output, delete the temporary result view in the input DMS
+    if type(output_0)==BufferedWriter:
+        View.delete_view(i_dms, o_view_name)
+
+    i_dms.close(force=True)
+    o_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/ecotag.cfiles

@@ -1,103 +0,0 @@
-../../../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

@@ -4,7 +4,7 @@ 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.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, str2bytes
@@ -12,6 +12,7 @@ from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
 import sys
+from io import BufferedWriter
 
 
 __title__="Taxonomic assignment of sequences"
@@ -22,6 +23,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
  
     group = parser.add_argument_group('obi ecotag specific options')
 
@@ -39,6 +41,17 @@ def addOptions(parser):
                       help="Minimum identity to consider for assignment, as a normalized identity, e.g. 0.95 for an identity of 95%%. "
                            "Default: 0.00 (no threshold).")
 
+    group.add_argument('--minimum-circle','-c',
+                      action="store", dest="ecotag:bubble_threshold",
+                      metavar='<CIRCLE_THRESHOLD>',
+                      default=0.99,
+                      type=float,
+                      help="Minimum identity considered for the assignment circle "
+                           "(sequence is assigned to the LCA of all sequences within a similarity circle of the best matches; "
+                           "the threshold for this circle is the highest value between <CIRCLE_THRESHOLD> and the best assignment score found for the query sequence). "
+                           "Give value as a normalized identity, e.g. 0.95 for an identity of 95%%. "
+                           "Default: 0.99.")
+
 def run(config):
         
     DMS.obi_atexit()
@@ -63,6 +76,10 @@ def run(config):
     ref_dms_name = ref[0].name
     ref_view_name = ref[1]
 
+    # Check that the threshold demanded is greater than or equal to the threshold used to build the reference database
+    if config['ecotag']['bubble_threshold'] < eval(ref_dms[ref_view_name].comments["ref_db_threshold"]) :
+        raise Exception(f"Error: The threshold demanded ({config['ecotag']['bubble_threshold']}) is lower than the threshold used to build the reference database ({float(ref_dms[ref_view_name].comments['ref_db_threshold'])}).")
+    
     # Open the output: only the DMS
     output = open_uri(config['obi']['outputURI'],
                       input=False,
@@ -70,17 +87,19 @@ def run(config):
     if output is None:
         raise Exception("Could not create output")
     o_dms = output[0]
+    output_0 = output[0]
     final_o_view_name = output[1]
     
-    # If 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
+    # If stdout output or the input and output DMS are not the same, create a temporary view that will be exported and deleted.
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
+        temporary_view_name = b"temp"
         i=0
         while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
-            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
             i+=1
         o_view_name = temporary_view_name
+        if type(output_0)==BufferedWriter:
+            o_dms = i_dms
     else:
         o_view_name = final_o_view_name
 
@@ -101,11 +120,12 @@ def run(config):
     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:
+    if obi_ecotag(i_dms.name_with_full_path, tobytes(i_view_name), \
+                  ref_dms.name_with_full_path, tobytes(ref_view_name), \
+                  taxo_dms.name_with_full_path, tobytes(taxonomy_name), \
+                  tobytes(o_view_name), comments, \
+                  config['ecotag']['threshold'], \
+                  config['ecotag']['bubble_threshold']) < 0:
         raise Exception("Error running ecotag")
     
     # If the input and output DMS are not the same, export result view to output DMS
@@ -115,15 +135,24 @@ def run(config):
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
+    # stdout output: write to buffer
+    if type(output_0)==BufferedWriter:
+        logger("info", "Printing to output...")
+        o_view = o_dms[o_view_name]
+        o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
+        o_view.close()
+
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
-    # If the input and the output DMS are different, delete the temporary result view in the input DMS
-    if i_dms != o_dms:
+    # If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
+    if i_dms != o_dms or type(output_0)==BufferedWriter:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    taxo_dms.close(force=True)
+    ref_dms.close(force=True)
+    i_dms.close(force=True)
     
     logger("info", "Done.")
 

python/obitools3/commands/export.cfiles

@@ -1,103 +0,0 @@
-../../../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

@@ -5,11 +5,19 @@ from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.dms import DMS
 from obitools3.dms.obiseq import Nuc_Seq
+from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
+from obitools3.writers.tab import TabWriter
+from obitools3.format.tab import TabFormat
+from obitools3.utils cimport tobytes, tostr
 
 from obitools3.apps.optiongroups import addMinimalInputOption, \
-                                        addExportOutputOption
+                                        addExportOutputOption, \
+                                        addNoProgressBarOption
 
 import sys
+import io
+
+from cpython.exc cimport PyErr_CheckSignals
 
 __title__="Export a view to a different file format"
 
@@ -18,6 +26,7 @@ def addOptions(parser):
     
     addMinimalInputOption(parser)
     addExportOutputOption(parser)
+    addNoProgressBarOption(parser)
 
 
 def run(config):
@@ -31,7 +40,16 @@ def run(config):
     if input is None:
         raise Exception("Could not read input")
     iview = input[1]
-            
+    
+    if 'outputformat' not in config['obi']:
+        if iview.type == b"NUC_SEQS_VIEW":
+            if QUALITY_COLUMN in iview:
+                config['obi']['outputformat'] = b'fastq'
+            else:
+                config['obi']['outputformat'] = b'fasta'
+        else:
+            config['obi']['outputformat'] = b'tabular'
+    
     # Open the output
     output = open_uri(config['obi']['outputURI'],
                       input=False)
@@ -44,26 +62,128 @@ def run(config):
      # 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)
     
+    if config['obi']['only'] is not None:
+        withoutskip = min(input[4], config['obi']['only'])
+    else:
+        withoutskip = input[4]
+     
+    if config['obi']['skip'] is not None:
+        skip = min(input[4], config['obi']['skip'])
+    else:
+        skip = 0
+    
+    # Initialize the progress bar
+    if config['obi']['noprogressbar']:
+        pb = None
+    else:
+        pb = ProgressBar(withoutskip - skip, config)
+
+    if config['obi']['outputformat'] == b'metabaR':
+        # Check prefix
+        if "metabarprefix" not in config["obi"]:
+            raise Exception("Prefix needed when exporting for metabaR (--metabaR-prefix option)")
+        else:
+            metabaRprefix = config["obi"]["metabarprefix"]
+        
     i=0
     for seq in iview :
-        pb(i)
+        PyErr_CheckSignals()
+        if pb is not None:
+            pb(i)
         try:
             writer(seq