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OBITools
Commit fca5fcdb authored by Eric Coissac's avatar Eric Coissac
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Preparing the 1.0.beta distribution

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.pydevproject
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......@@ -3,8 +3,8 @@
<pydev_project>
<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
<path>/OBITools/src</path>
<path>/OBITools/textwrangler</path>
<path>/OBITools-1.0/src</path>
<path>/OBITools-1.0/textwrangler</path>
</pydev_pathproperty>
<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python2.7</pydev_property>
......
.settings/org.eclipse.core.resources.prefs
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#Tue Oct 25 23:50:16 ICT 2011
eclipse.preferences.version=1
encoding//doc/sphinx/source/conf.py=utf-8
encoding//src/jwarcher2tab.py=iso-8859-1
encoding//src/obitools/carto/__init__.py=latin1
encoding//src/obitools/statistics/hypergeometric.py=UTF-8
doc/inout.dot deleted 100644 → 0
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digraph inout {
Graph [rankdir=TB,overlap=scale]
Node [shape="rectangle"];
subgraph cluster_fasta {
fasta [label="fasta\nsequence file",rank=1]
fastanuc [label="nucleic fasta",rank=2];
fastataxid [label="nucleic fasta\nwith taxid tag",rank=3];
fastapep [label="peptidic fasta",rank=2];
graph [rankdir=LR]
fastataxid -> fastanuc
fastapep -> fasta
fastanuc -> fasta
}
fasta454 [label="nucleic fasta\n454 sequencer (fna)",rank=3];
fastq [label="nucleic fastq\nwith quality"]
genbank [label="nucleic genbank file"]
embl [label="nucleic embl file"]
taxdump [label="NCBI Taxonomy dump\ntaxdump directory"]
ecopcrout [label="ecoPCR\nresult file"]
ecopcrdb [shape="record" label="{<DB> ecoPCR DB | {<Tax> Taxonomy| <Seq> Sequences}}"]
ecotagout [label="ecoTag.py\nresult file"]
ecotagabsfile [label="ecoTag.py\nabstract file"]
specificityrepport [label="taxonomy\nspecificity report"]
taxstatrepport [label="taxonomy\nstatistic report"]
rdataframe [label="R data frame\ntabular file"]
node [shape="oval"];
edge [arrowhead=open];
convert2fasta [label="convert2fasta.py"]
genbank -> convert2fasta [color=red]
embl -> convert2fasta [color=red]
fasta454 -> convert2fasta [color=red]
convert2fasta -> fastanuc [color=green]
ecopcr2fasta [label="ecopcr2fasta.py"]
ecopcrout -> ecopcr2fasta [color=red]
ecopcr2fasta -> fastanuc [color=green]
ecotag [label="ecoTag.py"]
fastanuc -> ecotag [color=red]
ecopcrdb:Tax -> ecotag [color=pink,style=dotted,label="taxonomy"]
fastataxid -> ecotag [color=pink,style=dotted,label="reference"]
ecotag -> ecotagout [color=green]
ecotagabstract [label="ecoTagAbstract.py"]
ecotagout -> ecotagabstract [color=red]
ecopcrdb -> ecotagabstract [color=pink,style=dotted,label="taxonomy"]
ecotagabstract -> ecotagabsfile [color=green]
ecotagmargeabstract [label="ecoTagMergeAbstract.py"]
ecotagabsfile -> ecotagmargeabstract [color=red]
ecotagabsfile -> ecotagmargeabstract [color=red]
ecotagabsfile -> ecotagmargeabstract [color=red]
ecotagmargeabstract -> rdataframe [color=green]
ecotaxspecificity [label="ecoTaxSpecificity.py"]
ecopcrout -> ecotaxspecificity [color=red]
ecopcrdb -> ecotaxspecificity [decorate,color=pink,style=dashed,label="taxonomy"]
ecotaxspecificity -> specificityrepport [color=green]
ecotaxstat [label="ecoTaxStat.py"]
ecopcrout -> ecotaxstat [color=red]
ecopcrdb -> ecotaxstat [color=pink,style=dotted,label="taxonomy"]
ecotaxstat -> taxstatrepport [color=green]
fasta454filter [label="fasta454Filter.py"]
fastanuc -> fasta454filter [color=red]
fasta454filter -> fastanuc [color=green]
fastacomplement [label="fastaComplement.py"]
fastanuc -> fastacomplement [color=red]
fastacomplement -> fastanuc [color=green]
fastacut [label="fastaCut.py"]
fasta -> fastacut [color=red]
fastacut -> fasta [color=green]
fastaannotate [label="fastaAnnotate.py"]
fasta -> fastaannotate [color=red]
fastaannotate -> fasta [color=green]
fastagrep [label="fastaGrep.py"]
fasta -> fastagrep [color=red]
fastagrep -> fasta [color=green]
fastalength [label="fastaLength.py"]
fasta -> fastalength [color=red]
fastalength -> fasta [color=green]
fastasplit [label="fastaSplit.py"]
fasta -> fastasplit [color=red]
fastasplit -> fasta [color=green]
fastasplit -> fasta [color=green]
fastasplit -> fasta [color=green]
fastauniq [label="fastaUniq.py"]
fasta -> fastauniq [color=red]
fastauniq -> fasta [color=green]
ecopcrformat [label="ecoPCRFormat.py", URL="/trac/ecoPCR"]
genbank -> ecopcrformat [color=red]
embl -> ecopcrformat [color=red]
fastataxid -> ecopcrformat [color=red]
ecopcrformat -> ecopcrdb:DB [color=green]
buildobitaxonomy [label="buildOBITaxonomy.py"]
taxdump -> buildobitaxonomy [color=red]
buildobitaxonomy -> ecopcrdb:Tax [color=green]
ecopcr [label="ecoPCR", URL="/trac/ecoPCR"]
ecopcrdb:DB -> ecopcr [color=red]
ecopcr -> ecopcrout [color=green]
}
\ No newline at end of file
doc/inout.map deleted 100644 → 0
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<area shape="poly" id="node77" href="/trac/ecoPCR" title="ecoPCRFormat.py" alt="" coords="958,128 953,121 938,114 916,109 887,105 855,104 823,105 794,109 771,114 756,121 751,128 756,135 771,142 794,147 823,151 855,152 887,151 916,147 938,142 953,135">
<area shape="poly" id="node85" href="/trac/ecoPCR" title="ecoPCR" alt="" coords="1458,355 1455,347 1448,341 1436,335 1421,332 1404,331 1387,332 1372,335 1360,341 1353,347 1350,355 1353,362 1360,369 1372,374 1387,377 1404,379 1421,377 1436,374 1448,369 1455,362">
doc/oligoTag/Makefile deleted 100644 → 0
View file @ ad4c8408
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = build
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
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 " 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 " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
clean:
-rm -rf $(BUILDDIR)/*
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
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/oligoTag.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/oligoTag.qhc"
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
"run these through (pdf)latex."
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."
doc/oligoTag/make.bat deleted 100644 → 0
View file @ ad4c8408
@ECHO OFF
REM Command file for Sphinx documentation
set SPHINXBUILD=sphinx-build
set BUILDDIR=build
set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source
if NOT "%PAPER%" == "" (
set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
)
if "%1" == "" goto help
if "%1" == "help" (
: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. 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. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
echo. changes to make an overview over all changed/added/deprecated items
echo. linkcheck to check all external links for integrity
echo. doctest to run all doctests embedded in the documentation if enabled
goto end
)
if "%1" == "clean" (
for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
del /q /s %BUILDDIR%\*
goto end
)
if "%1" == "html" (
%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/html.
goto end
)
if "%1" == "dirhtml" (
%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
goto end
)
if "%1" == "pickle" (
%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
echo.
echo.Build finished; now you can process the pickle files.
goto end
)
if "%1" == "json" (
%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
echo.
echo.Build finished; now you can process the JSON files.
goto end
)
if "%1" == "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.
goto end
)
if "%1" == "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\oligoTag.qhcp
echo.To view the help file:
echo.^> assistant -collectionFile %BUILDDIR%\qthelp\oligoTag.ghc
goto end
)
if "%1" == "latex" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
echo.
echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "changes" (
%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
echo.
echo.The overview file is in %BUILDDIR%/changes.
goto end
)
if "%1" == "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.
goto end
)
if "%1" == "doctest" (
%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
echo.
echo.Testing of doctests in the sources finished, look at the ^
results in %BUILDDIR%/doctest/output.txt.
goto end
)
:end
doc/oligoTag/source/conf.py deleted 100644 → 0
View file @ ad4c8408
# -*- coding: utf-8 -*-
#
# oligoTag documentation build configuration file, created by
# sphinx-quickstart on Tue Feb 9 11:30:02 2010.
#
# 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, os
# 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.append(os.path.abspath('.'))
# -- General configuration -----------------------------------------------------
# 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.pngmath']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'oligoTag'
copyright = u'2010, Eric Coissac'
# 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 = '1.0'
# The full version, including alpha/beta/rc tags.
release = '1.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#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 documents that shouldn't be included in the build.
#unused_docs = []
# List of directories, relative to source directory, that shouldn't be searched
# for source files.
exclude_trees = []
# 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 = []
# -- Options for HTML output ---------------------------------------------------
# The theme to use for HTML and HTML Help pages. Major themes that come with
# Sphinx are currently 'default' and 'sphinxdoc'.
html_theme = 'default'
# 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']
# 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_use_modindex = 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, 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 = ''
# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = ''
# Output file base name for HTML help builder.
htmlhelp_basename = 'oligoTagdoc'
# -- Options for LaTeX output --------------------------------------------------
# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'
# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('index', 'oligoTag.tex', u'oligoTag Documentation',
u'Eric Coissac', '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
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_use_modindex = True
doc/oligoTag/source/index.rst deleted 100644 → 0
View file @ ad4c8408
.. oligoTag documentation master file, created by
sphinx-quickstart on Tue Feb 9 11:30:02 2010.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
OligoTag's documentation!
=========================
Contents:
.. toctree::
:maxdepth: 2
Overview
--------
Sequencing a huge number of PCR amplicons using high throughput sequencing platforms
involves using sample-specific oligonucleotide tags for allowing sample multiplexing and
sorting out of the sequences during the data processing. OligoTags helps in designing
sets of tags. Several parameters allow users to define the characteristics of the
generated tags in term of family size, tag length, minimal distance between them,
GC content and presence of homopolymers.
OligoTags is based on the clique notion from the graph theory.
To determine the tags properties you should take into account severals experiment parameter.