Commit 3374a79c by Frédéric Boyer

Edited the obicomplement and obiselect doc

parent e951ca7f
......@@ -8,5 +8,6 @@ Sequence sampling and filtering
scripts/obitail
scripts/obigrep
scripts/obisample
scripts/obiselect
\ No newline at end of file
Computations on sequences
=========================
.. toctree::
:maxdepth: 2
scripts/obicomplement
......@@ -14,5 +14,6 @@ Contents:
conversions
annotations
manipulations
filtering
statistics
Extract the first sequences from a sequence file
================================================
Reverse complement the sequences from a sequence file
=====================================================
Print tail of a sequence file. Can specify number of sequences to be printed.
Print the reverse complement of the sequences of a sequence file.
.. include:: ../optionsSet/defaultoptions.txt
......
.. automodule:: obigrep
.. include:: ../optionsSet/defaultoptions.txt
.. include:: ../optionsSet/inputformat.txt
.. cmdoption:: -v, --inverse-match
revert the sequence selection [default : False]
......@@ -2,7 +2,7 @@
'''
`obiannotate` : Add/Edit annotations of sequences in a sequence file
=====================================
====================================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
#!/usr/local/bin/python
"""
`obicomplement` : Reverse complement sequences
==============================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
:py:mod:`obicomplement` command allows to reverse complement the sequences in a file.
Note that the identifiers 'ID' of the sequences are modified and are of the form 'ID_CMP'.
Example:
.. code-block:: bash
> obicomplement seq.fasta > seqRC.fasta
"""
from obitools.options import getOptionManager
from obitools.options.bioseqfilter import addSequenceFilteringOptions
......@@ -9,7 +25,7 @@ from obitools.format.options import addInOutputOption, sequenceWriterGenerator
if __name__=='__main__':
optionParser = getOptionManager([addSequenceFilteringOptions,addInOutputOption])
optionParser = getOptionManager([addSequenceFilteringOptions,addInOutputOption], progdoc=__doc__)
(options, entries) = optionParser()
......
#!/usr/local/bin/python
'''
Created on 6 juil. 2010
"""
`obiselect` : Select and print sequences identified by a list of IDs
=====================================================================
@author: coissac
'''
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
:py:mod:`obiselect` command allows to select a set of sequences identified by a list of IDs.
Note that the supplied identifiers are not required to correspond to any existing sequence identifier.
If an ID is not found, no warning will be produced.
Option -v allows to invert the selection and thus select sequences whose IDs are not in the list.
Example:
.. code-block:: bash
> obiselect --identifier IDs.list seq.fasta > selectedSeq.fasta
"""
from obitools.format.options import addInOutputOption, sequenceWriterGenerator
from obitools.options import getOptionManager
from obitools.format.sequence import autoSequenceIterator
def addSelectOptions(optionManager):
......@@ -27,7 +41,7 @@ def addSelectOptions(optionManager):
if __name__ == '__main__':
optionParser = getOptionManager([addSelectOptions,addInOutputOption])
optionParser = getOptionManager([addSelectOptions,addInOutputOption], progdoc=__doc__)
(options, entries) = optionParser()
......
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