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.. automodule:: obiextract
:py:mod:`obiextract` specific options
-------------------------------------
.. cmdoption:: -s <KEY>, --sample=<KEY>
Attribute containing sample descriptions. By default the attribute
name used for describing samples is set to ``merged_sample``.
.. cmdoption:: -e <SAMPLE_NAME>, --extract=<KEY>
Attribute indicating which <SAMPLE_NAME> have to be extracted.
Several ``-p`` options can be added for specifying several samples.
If you want to extract a large number of samples, please refer to the ``-E``
option described below
.. TIP:: The ``<KEY>`` can be simply the key of an attribute, or a *Python* expression
similarly to the ``-p`` option of :py:mod:`obigrep`.
*Example:*
.. code-block:: bash
> obiextract -e sampleA -e sampleB allseqs.fasta > samplesAB.fasta
This command extracts from the ``allseqs.fasta`` file data related to samples ``A`` and ``B``.
.. cmdoption:: -E <FILENAME>, --extract-list=<FILENAME>
Allows for indicating a file name where a list of sample is stored. The file must be a simple
text file with a sample name per line.
*Example:*
.. code-block:: bash
> obiextract -E subset.txt allseqs.fasta > subset_samples.fasta
This command extracts from the ``allseqs.fasta`` file data related to samples listed in the ``subset.txt`` file.
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/outputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
:py:mod:`obiextract` modified sequence attributes
-------------------------------------------------
- :doc:`count <../attributes/count>`
:py:mod:`obiextract` used sequence attribute
--------------------------------------------
- :doc:`count <../attributes/count>`
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