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Cleaning of the doc, but far to e finished

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Eric Coissac
2013-12-24 12:48:22 +00:00
parent d674808d56
commit 4fe1c167ef
48 changed files with 241 additions and 83 deletions
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15
doc/sphinx/api/graph/algorithms/component.rst Normal file
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.. automodule:: obitools.graph.algorithms.component
Functions
^^^^^^^^^
Connected component iterator
............................
.. autofunction:: componentIterator
Counting connected component in a graph
.......................................
.. autofunction:: componentCount

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Algorithms applicable to graphs
===============================
the module :py:mod:`obitools.graph.algoriths` provides a set of algorithms
applicable to :py:class:`obitools.graph.Graph` instances.
.. toctree::
:maxdepth: 2
clique
component
compact

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Graph representation
====================
.. toctree::
:maxdepth: 2
dag
unrooted
algorithms/index
layout/index
.. automodule:: obitools.graph
Classes
^^^^^^^
Basic graph
...........
.. autoclass:: Graph
:members:
Directed graph
..............
.. autoclass:: DiGraph
:members:
Undirected graph
................
.. autoclass:: UndirectedGraph
:members:
The nodes or vertice of a graph
...............................
.. autoclass:: Node
:members:
The edges of a graph
....................
.. autoclass:: Edge
:members:
The Indexer utility class
.........................
.. autoclass:: Indexer
:members:
.. automethod:: __getitem__
.. automethod:: __equal__

0
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0
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obitools module programming interface
=====================================
.. toctree::
:maxdepth: 2
sequences/index
graph/index

57
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@ -0,0 +1,57 @@
Biological sequences representation
===================================
.. toctree::
:maxdepth: 2
.. automodule:: obitools
Classes
^^^^^^^
Abstract class for all biological sequences
...........................................
.. autoclass:: BioSequence
:members:
Nucleic (DNA) sequences
.......................
.. autoclass:: NucSequence
:members:
Amino-acid sequences
.....................
.. autoclass:: AASequence
:members:
Biological sequences as the transformation of others sequences
..............................................................
.. autoclass:: WrappedBioSequence
:members:
Fragment of sequences
.....................
.. autoclass:: SubSequence
:members:
Reversed complemented DNA sequences
...................................
.. autoclass:: DNAComplementSequence
:members:
Functions
^^^^^^^^^
.. autofunction:: bioSeqGenerator

9
doc/sphinx/source/attributes.rst
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@ -10,7 +10,9 @@ Contents:
:maxdepth: 2
attributes/count
attributes/cut
attributes/direction
attributes/error
attributes/family
attributes/family_name
attributes/forward_match
@ -21,13 +23,18 @@ Contents:
attributes/mode
attributes/order
attributes/order_name
attributes/pairend_limit
attributes/rank
attributes/reverse_match
attributes/reverse_primer
attributes/reverse_tag
attributes/scientific_name
attributes/score
attributes/seq_length
attributes/sminL
attributes/sminR
attributes/species
attributes/species_name
attributes/score
attributes/status
attributes/taxid

16
doc/sphinx/source/attributes/count.rst
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@ -4,13 +4,13 @@ count
An integer value indicating how many times this sequence occurs in the dataset.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obisample <scripts/obisample>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`
Attribute used by the programs:
- :doc:`ecotag <scripts/ecotag>`
- :doc:`ecotaxspecificity <scripts/ecotaxspecificity>`
- :doc:`obiclean <scripts/obiclean>`
- :doc:`obicount <scripts/obicount>`
- :doc:`obisample <scripts/obisample>`
- :doc:`obistat <scripts/obistat>`
- :doc:`ecotag <../scripts/ecotag>`
- :doc:`ecotaxspecificity <../scripts/ecotaxspecificity>`
- :doc:`obiclean <../scripts/obiclean>`
- :doc:`obicount <../scripts/obicount>`
- :doc:`obisample <../scripts/obisample>`
- :doc:`obistat <../scripts/obistat>`

2
doc/sphinx/source/attributes/cut.rst
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@ -6,6 +6,6 @@ cut
Attribute added by the programs:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

4
doc/sphinx/source/attributes/direction.rst
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@ -2,13 +2,13 @@ direction
=========
Attribute added by the program:
- :doc:`illuminapairedend <scripts/illuminapairedend>`
- :doc:`illuminapairedend <../scripts/illuminapairedend>`
Either 'left' or 'right'. Indicates the way the alignment has been done, and especially where
the overlapping part is located on the forward read (either its 'right' part, or its
'left' part).
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`
Either 'forward' or 'reverse'. Indicates if the primers have been identified on the 'forward' or
'reverse' strand.

2
doc/sphinx/source/attributes/error.rst
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@ -6,6 +6,6 @@ error
Attribute added by the programs:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

4
doc/sphinx/source/attributes/family.rst
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@ -7,11 +7,11 @@ family
.. warning:: This taxonomic information is just added to the sequence for the end-user
convenience and not used by other ``obitool`` programs as taxonomic information.
Only the taxonomic information included in the :doc:`taxid <../attributes/taxid>`
Only the taxonomic information included in the :doc:`taxid <taxid>`
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

6
doc/sphinx/source/attributes/family_name.rst
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@ -2,16 +2,16 @@ family_name
===========
A string value indicating the family name of the taxid stored into the
:doc:`taxid <attributes/taxid>`. If the family is not defined for this taxid,
:doc:`taxid <taxid>`. If the family is not defined for this taxid,
this value is *None*.
.. warning:: This taxonomic information is just added to the sequence for the end-user
convenience and not used by other ``obitool`` programs as taxonomic information.
Only the taxonomic information included in the :doc:`taxid <../attributes/taxid>`
Only the taxonomic information included in the :doc:`taxid <taxid>`
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

2
doc/sphinx/source/attributes/forward_match.rst
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@ -5,6 +5,6 @@ forward_match
the sequence.
Attribute added by the program:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

2
doc/sphinx/source/attributes/forward_primer.rst
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@ -4,5 +4,5 @@ forward_primer
A string value indicating the forward primer used to obtain the sequence.
Attribute added by the program:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

2
doc/sphinx/source/attributes/forward_tag.rst
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@ -5,6 +5,6 @@ forward_tag
forward primer and used to assign the sequence to a sample.
Attribute added by the program:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

4
doc/sphinx/source/attributes/genus.rst
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@ -9,11 +9,11 @@ genus
.. warning:: This taxonomic information is just added to the sequence for the end-user
convenience and not used by other ``obitool`` programs as taxonomic information.
Only the taxonomic information included in the :doc:`taxid <../attributes/taxid>`
Only the taxonomic information included in the :doc:`taxid <taxid>`
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

6
doc/sphinx/source/attributes/genus_name.rst
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@ -2,15 +2,15 @@ genus_name
==========
A string value indicating the genus name of the taxid stored into the
:doc:`taxid <attributes/taxid>`. If the genus is not defined for this taxid,
:doc:`taxid <taxid>`. If the genus is not defined for this taxid,
this value is *None*.
.. warning:: This taxonomic information is just added to the sequence for the end-user
convenience and not used by other ``obitool`` programs as taxonomic information.
Only the taxonomic information included in the :doc:`taxid <../attributes/taxid>`
Only the taxonomic information included in the :doc:`taxid <taxid>`
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

2
doc/sphinx/source/attributes/mode.rst
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@ -5,7 +5,7 @@ mode
aligned reads ('alignment') or just the concatenation of the two reads ('joined').
Attribute added by the program:
- :doc:`illuminapairedend <scripts/illuminapairedend>`
- :doc:`illuminapairedend <../scripts/illuminapairedend>`

4
doc/sphinx/source/attributes/order.rst
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@ -7,10 +7,10 @@ order
.. warning:: This taxonomic information is just added to the sequence for the end-user
convenience and not used by other ``obitool`` programs as taxonomic information.
Only the taxonomic information included in the :doc:`taxid <../attributes/taxid>`
Only the taxonomic information included in the :doc:`taxid <taxid>`
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

6
doc/sphinx/source/attributes/order_name.rst
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@ -2,14 +2,14 @@ order_name
==========
A string value indicating the order name of the taxid stored into the
:doc:`taxid <attributes/taxid>`. If the order is not defined for this taxid,
:doc:`taxid <taxid>`. If the order is not defined for this taxid,
this value is *None*.
.. warning:: This taxonomic information is just added to the sequence for the end-user
convenience and not used by other ``obitool`` programs as taxonomic information.
Only the taxonomic information included in the :doc:`taxid <../attributes/taxid>`
Only the taxonomic information included in the :doc:`taxid <taxid>`
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

2
doc/sphinx/source/attributes/pairend_limit.rst
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@ -5,5 +5,5 @@ pairend_limit
the position in the reported sequence where the second read starts.
Attribute added by the program:
- :doc:`illuminapairedend <scripts/illuminapairedend>`
- :doc:`illuminapairedend <../scripts/illuminapairedend>`

2
doc/sphinx/source/attributes/rank.rst
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@ -10,6 +10,6 @@ rank
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

2
doc/sphinx/source/attributes/reverse_match.rst
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@ -5,6 +5,6 @@ reverse_match
the sequence.
Attribute added by the program:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

2
doc/sphinx/source/attributes/reverse_primer.rst
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@ -4,6 +4,6 @@ reverse_primer
A string value indicating the reverse primer used to obtain the sequence.
Attribute added by the program:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

2
doc/sphinx/source/attributes/reverse_tag.rst
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@ -5,5 +5,5 @@ reverse_tag
reverse primer and used to assign the sequence to a sample.
Attribute added by the program:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

2
doc/sphinx/source/attributes/scientific_name.rst
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@ -11,6 +11,6 @@ scientific_name
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

2
doc/sphinx/source/attributes/score.rst
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@ -4,5 +4,5 @@ score
A real value computed based on the alignment of two paired-end reads.
Attribute added by the program:
- :doc:`illuminapairedend <scripts/illuminapairedend>`
- :doc:`illuminapairedend <../scripts/illuminapairedend>`

4
doc/sphinx/source/attributes/seq_length.rst
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@ -4,7 +4,7 @@ seq_length
A integer value indicating the length of the sequence
Attribute added by the programs:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`obiannotate <scripts/obiannotate>`
- :doc:`ngsfilter <../scripts/ngsfilter>`
- :doc:`obiannotate <../scripts/obiannotate>`

2
doc/sphinx/source/attributes/sminL.rst
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@ -5,4 +5,4 @@ sminL
which ``left`` alignment are discarded.
Attribute added by the programs:
- :doc:`illuminapairedend <scripts/illuminapairedend>`
- :doc:`illuminapairedend <../scripts/illuminapairedend>`

2
doc/sphinx/source/attributes/sminR.rst
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@ -5,4 +5,4 @@ sminR
which ``right`` alignment are discarded.
Attribute added by the programs:
- :doc:`illuminapairedend <scripts/illuminapairedend>`
- :doc:`illuminapairedend <../scripts/illuminapairedend>`

4
doc/sphinx/source/attributes/species.rst
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@ -7,11 +7,11 @@ species
.. warning:: This taxonomic information is just added to the sequence for the end-user
convenience and not used by other ``obitool`` programs as taxonomic information.
Only the taxonomic information included in the :ref:`taxid`
Only the taxonomic information included in the :doc:`taxid <taxid>`
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

6
doc/sphinx/source/attributes/species_name.rst
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@ -2,16 +2,16 @@ species_name
============
A string value indicating the species name of the taxid stored into the
:doc:`taxid <attributes/taxid>`. If the species is not defined for this taxid,
:doc:`taxid <taxid>`. If the species is not defined for this taxid,
this value is *None*.
.. warning:: This taxonomic information is just added to the sequence for the end-user
convenience and not used by other ``obitool`` programs as taxonomic information.
Only the taxonomic information included in the :doc:`taxid <../attributes/taxid>`
Only the taxonomic information included in the :doc:`taxid <taxid>`
attribute is used as taxonomic annotation.
Attribute added by the programs:
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiuniq <../scripts/obiuniq>`
- :doc:`obisample <../scripts/obisample>`

2
doc/sphinx/source/attributes/status.rst
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@ -5,6 +5,6 @@ status
Attribute added by the programs:
- :doc:`ngsfilter <scripts/ngsfilter>`
- :doc:`ngsfilter <../scripts/ngsfilter>`

16
doc/sphinx/source/attributes/taxid.rst
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@ -4,15 +4,15 @@ taxid
An integer referring unambiguously to one taxon in the taxonomic associated database
Attribute added by the programs:
- :doc:`ecotag <scripts/ecotag>`
- :doc:`ecopcr <scripts/ecotag>`
- :doc:`obiaddtaxids <scripts/obiaddtaxids>`
- :doc:`ecotag <../scripts/ecotag>`
- :doc:`ecopcr <../scripts/ecotag>`
- :doc:`obiaddtaxids <../scripts/obiaddtaxids>`
Attribute used by the programs:
- :doc:`obiselect <scripts/ecotag>`
- :doc:`obiannotate <scripts/obiannotate>`
- :doc:`ecodbtaxstat <scripts/ecodbtaxstat>`
- :doc:`ecotaxspecificity <scripts/ecotaxspecificity>`
- :doc:`obiuniq <scripts/obiuniq>`
- :doc:`obiselect <../scripts/ecotag>`
- :doc:`obiannotate <../scripts/obiannotate>`
- :doc:`ecodbtaxstat <../scripts/ecodbtaxstat>`
- :doc:`ecotaxspecificity <../scripts/ecotaxspecificity>`
- :doc:`obiuniq <../scripts/obiuniq>`

10
doc/sphinx/source/conf.py
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@ -60,7 +60,7 @@ master_doc = 'index'
# General information about the project.
project = u'OBITools'
copyright = u'2009 - 2013, Eric Coissac'
copyright = u'2009 - 2013, OBITool Development Team'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@ -187,24 +187,26 @@ htmlhelp_basename = 'OBIToolsdoc'
# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'
latex_paper_size = 'a4'
# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'
latex_font_size = '11pt'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('index', 'OBITools.tex', u'OBITools Documentation',
u'Eric Coissac', 'manual'),
u'OBITools Development Team', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
latex_logo = 'OBITools.png'
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
latex_use_parts = True
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''

4
doc/sphinx/source/scripts/ecoPrimers.rst
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@ -227,11 +227,11 @@ Examples
> ecoPrimers -d mydatabase -e 2 -l 30 -L 120 -r 7742 - i 2 -E 9604 -3 2 > mybarcodes.ecoprimers
Launches a search for barcodes and corresponding primers on mydatabase (in the ``ecoPCR format``,
Launches a search for barcodes and corresponding primers on mydatabase (in the `ecoPCR format`,
see :py:mod:`obiconvert`), with a maximum of two mismatches for each primer. The minimum and
maximum barcode lengths (excluding primers) are 30 bp and 120 bp, respectively. The search is
restricted to the Vertebrates, excluding Bacteria and Hominidae (7742, 2, and 9604 corresponds to
the ``TAXID``of Vertebrates, Bacteria, and Hominidae, respectively. The two last nucleotides on
the `TAXID` of Vertebrates, Bacteria, and Hominidae, respectively. The two last nucleotides on
the 3' end of the primers must have a perfect match with their target sequences. The results
are saved in the mybarcodes.ecoprimers file.

4
doc/sphinx/source/scripts/ecopcr2fasta.rst
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@ -1,4 +0,0 @@
Convert ecoPCR result files to extended OBITools fasta file
===========================================================
.. include:: ../optionsSet/defaultoptions.txt

8
doc/sphinx/source/scripts/ecotaxspecificity.rst
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@ -10,12 +10,12 @@
*Example:*
.. code-block:: bash
.. code-block:: bash
> ecotaxspecificity -d my_ecopcr_database -e 5 seq.fasta
> ecotaxspecificity -d my_ecopcr_database -e 5 seq.fasta
This command considers that two sequences with less than 5 differences
correspond to the same barcode.
This command considers that two sequences with less than 5 differences
correspond to the same barcode.
.. include:: ../optionsSet/taxonomyDB.txt

13
doc/sphinx/source/wolves.rst
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@ -63,12 +63,17 @@ The data needed to reproduce the tutorial are the following:
- the :doc:`fastq <fastq>` files resulting of the Illumina paired-end sequencing assay of DNA extracted and amplified from
the wolves feces and other samples (not described here)
the wolves feces and other samples (not described here) :
* ``YG_BIOSP_7_1_612GNAAXX.fastq``
* ``YG_BIOSP_7_2_612GNAAXX.fastq``
- the file describing the primers and tags used for all samples sequenced in the seventh region of the Illumina run
- the file describing the primers and tags used for all samples sequenced in the seventh region of the Illumina run :
* ``NGS-R7.txt``
- the EMBL nucleotide distribution and the NCBI taxonomy formatted in the ecoPCR_ format (see the `obiconvert <scripts/obiconvert>` utility for details)
- the EMBL nucleotide distribution and the NCBI taxonomy formatted in the ecoPCR_ format (see the `obiconvert <scripts/obiconvert>` utility for details) :
* ``embl_r107*``
@ -203,7 +208,7 @@ it is convenient to work with uniq *sequences* instead of *reads*. To *dereplica
+-------------------------------------------------------------+
We use the :py:mod:`obiuniq` command with the ``-m sample``. The ``-m sample``option is used to keep the information of the samples of origin for each sequence.
We use the :py:mod:`obiuniq` command with the `-m sample`. The `-m sample` option is used to keep the information of the samples of origin for each sequence.
.. code-block:: bash

2
src/ecotag.py
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@ -95,7 +95,7 @@ def addSearchOptions(optionManager):
optionManager.add_option('-u','--uniq',
action='store_true',dest='uniq',
default=False,
help='Apply uniq filter on sequences before identification')
help='Apply a uniq filter on query sequences before identification')
# optionManager.add_option('-T','--table',
# action='store_true',dest='table',

2
src/ecotaxstat.py
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@ -5,7 +5,7 @@
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
The :py:mod:`ecotaxstat` command requires two parameters : an ecoPCR formatted database (specified with the ``-d``option)
The :py:mod:`ecotaxstat` command requires two parameters : an ecoPCR formatted database (specified with the `-d` option)
and an ecoPCR output (ideally computed using the specified ecoPCR database).
The command outputs for every ranks the coverage of the ecoPCR output, that is the fraction of taxids that

4
src/obigrep.py
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@ -5,9 +5,9 @@
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
The :py:mod:`obigrep` command is in some way analog to the standard Unix ``grep``
The :py:mod:`obigrep` command is in some way analog to the standard Unix `grep`
command.
It selects a subset of sequence records from a :ref:`sequence file <../format>`.
It selects a subset of sequence records from a :doc:`sequence file <../formats>`.
A sequence record is a :doc:`complex object <../fasta>` composed of an identifier,
a set of attributes (``key=value``), a definition, and the sequence itself.

2
src/obihead.py
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@ -6,7 +6,7 @@
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
:py:mod:`obihead` command is in some way analog to the standard Unix `head` command.
It selects the head of :ref:`a sequence file <../format>`.
It selects the head of :doc:`a sequence file <../formats>`.
But instead of working text line by text line as the standard Unix tool,
selection is done at the sequence record level. You can specify the number of sequence records
to select.

2
src/obitail.py
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@ -6,7 +6,7 @@
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
:py:mod:`obitail` command is in some way analog to the standard Unix `tail` command.
It selects the tail of :ref:`a sequence file <../format>`.
It selects the tail of :doc:`a sequence file <../formats>`.
But instead of working text line by text line as the standard Unix tool,
selection is done at the sequence record level. You can specify the number of
sequence records to select.

4
src/obitools/version.py
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@ -1,5 +1,5 @@
major = 1
minor = 0
serial= 'beta'
serial= 'beta 2'
version = "%02d.%02d.%s" % (major,minor,serial)
version = "%2d.%02d %s" % (major,minor,serial)