82 lines
2.1 KiB
ReStructuredText
82 lines
2.1 KiB
ReStructuredText
.. automodule:: obisubset
|
|
|
|
|
|
:py:mod:`obisubset` specific options
|
|
------------------------------------
|
|
|
|
.. cmdoption:: -s <TAGNAME>, --sample=<TAGNAME>,
|
|
|
|
The option ``-s`` allows to specify the tag containing sample descriptions,
|
|
the default value is set to *merged_sample*.
|
|
|
|
*Example:*
|
|
|
|
.. code-block:: bash
|
|
|
|
> obiuniq -m sample seq1.fasta > seq2.fasta
|
|
> obisubset -s merged_sample -n sample1 seq2.fasta > seq3.fasta
|
|
|
|
After the dereplication of the sequences using the
|
|
in the new attribute ``merged_sample``.
|
|
|
|
.. cmdoption:: -o <TAGNAME>, --other-tag=<TAGNAME>,
|
|
|
|
Another tag to clean according to the sample subset
|
|
|
|
*Example:*
|
|
|
|
.. code-block:: bash
|
|
|
|
> obisubset -s merged_sample -o -n sample1 seq2.fasta > seq3.fasta
|
|
|
|
.. cmdoption:: -l <FILENAME>, --sample-list=<FILENAME>,
|
|
|
|
File containing the samples names (one sample id per line).
|
|
|
|
*Example:*
|
|
|
|
.. code-block:: bash
|
|
|
|
> obisubset -s merged_sample -o -l ids.txt seq2.fasta > seq3.fasta
|
|
|
|
.. cmdoption:: -p <REGEX>, --sample-pattern=<REGEX>,
|
|
|
|
A regular expression pattern matching the sample ids to extract.
|
|
|
|
*Example:*
|
|
|
|
.. code-block:: bash
|
|
|
|
> obisubset -s merged_sample -o -p "negative_.*" seq2.fasta > seq3.fasta
|
|
|
|
.. cmdoption:: -n <SAMPLEIDS>, --sample-name=<SAMPLEIDS>,
|
|
|
|
A sample id to extract
|
|
|
|
*Example:*
|
|
|
|
.. code-block:: bash
|
|
|
|
> obisubset -s merged_sample -o -n sample1 seq2.fasta > seq3.fasta
|
|
|
|
.. include:: ../optionsSet/inputformat.txt
|
|
|
|
.. include:: ../optionsSet/outputformat.txt
|
|
|
|
.. include:: ../optionsSet/defaultoptions.txt
|
|
|
|
:py:mod:`obisubset` modifies sequence attributes
|
|
------------------------------------------------
|
|
|
|
.. hlist::
|
|
:columns: 3
|
|
|
|
- :doc:`count <../attributes/count>`
|
|
- :doc:`merged_* <../attributes/merged_star>`
|
|
|
|
:py:mod:`obisubset` used sequence attribute
|
|
-------------------------------------------
|
|
|
|
- :doc:`count <../attributes/taxid>`
|
|
- :doc:`merged_* <../attributes/merged_star>`
|