Commit 2bfa8f75 by Eric Coissac

Add obiselect and obijoinpairedend documentation

parent 51a4be62
#!/usr/local/bin/python
'''
:py:mod:`illuminapairedend`: aligns paired end Illumina reads
=============================================================================================================================
=============================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
#!/usr/local/bin/python
'''
Created on 30 dec. 2009
:py:mod:`obijoinpairedend`: joins paired end reads
==================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
:py:mod:`obijoinpairedend` aims at joining the two reads of a paired-end library.
For this purpose, it concatenates sequence merging the forward read and the
reversed-complemented reverse read. A stretch of N is added between both the reads.
The program uses as input one or two sequences reads files.
- If two files are used one of them must be specified using the ``-r`` option.
Sequence records corresponding to the same read pair must be in the same order
in the two files.
- If just one file is provided, sequence records are supposed to be all of the same length.
The first half of the sequence is used as forward read, the second half is used as the reverse
read.
*Example:*
.. code-block:: bash
> obijoinpairedend -r seq3P.fastq seq5P.fastq > seq.fastq
The ``seq5P.fastq`` sequence file contains the forward sequence records.
The ``seq3P.fastq`` sequence file contains the reverse sequence records.
Pairs of reads are joined together and the resulting sequence is stored in the
`` seq.fastq`` file.
@author: coissac
'''
from obitools.options import getOptionManager
......
#!/usr/local/bin/python
"""
:py:mod:`obiselect` : Select and print sequences identified by a list of IDs
============================================================================
:py:mod:`obiselect` : Selects representative sequences from a sequence file
===========================================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
:py:mod:`obiselect` command allows to select a set of sequences
Example:
:py:mod:`obiselect` command allows to select a subset of sequences records from a sequence
file by describing sequence record groups and defining how many and which sequence records
from each group must be retrieved.
.. code-block:: bash
> obiselect ...
Example:
.. code-block:: bash
> obiselect ...
The above command splits the sequence input file according to the ``mode`` attribute.
This attribute is created by the :py:mod:`solexapairend` tool and its value can be set to
either ``joined`` or ``alignment``. The prefix ``experiment_`` is put before
each subfile name. Two subfiles will thus be created: ``experiment_joined`` and
``experiment_alignment``.
"""
from obitools.format.options import addInOutputOption, sequenceWriterGenerator,\
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment