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.. 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>`
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