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.. automodule:: obistat
:py:mod:`obistat` specific options
----------------------------------
.. cmdoption:: -c <KEY>, --category-attribute=<KEY>
Attribute used to categorize the sequence records. Several ``-c`` options can be combined.
.. 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
> obistat -c sample -c seq_length seq.fasta
This command prints the number of sequence records and total count for each combination of
sample and sequence length.
.. cmdoption:: -m <KEY>, --min=<KEY>
Computes the minimum value of attribute <KEY> for each category.
*Example:*
.. code-block:: bash
> obistat -c sample -m seq_length seq.fastq
This command computes the minimum sequence length observed for each sample.
.. cmdoption:: -M <KEY>, --max=<KEY>
Computes the maximum value of attribute <KEY> for each category.
*Example:*
.. code-block:: bash
> obistat -c sample -M seq_length seq.fastq
This command computes the maximum sequence length observed for each sample.
.. cmdoption:: -a <KEY>, --mean=<KEY>
Computes the mean value of attribute <KEY> for each category.
*Example:*
.. code-block:: bash
> obistat -c sample -a seq_length seq.fastq
This command computes the mean sequence length observed for each sample.
.. cmdoption:: -v <KEY>, --variance=<KEY>
Computes the variance of attribute <KEY> for each category.
*Example:*
.. code-block:: bash
> obistat -c genus_name -v reverse_error seq.fastq
This command computes the variance of the number of errors observed in the reverse primer for each genus.
.. cmdoption:: -s <KEY>, -std-dev=<KEY>
Computes the standard deviation of attribute <KEY> for each category.
*Example:*
.. code-block:: bash
> obistat -c genus_name -s reverse_error seq.fastq
This command computes the standard deviation of the number of errors observed in the reverse primer for each genus.
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/taxonomyDB.txt
.. include:: ../optionsSet/defaultoptions.txt
:py:mod:`obistat` used sequence attribute
-----------------------------------------
- :doc:`count <../attributes/count>`
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