extract_shared_or_unique_otuids.py
==================================

Parse a BIOM format file and obtain a list of unique OTUIDs found in each category in mapping file.

    .. code-block:: bash

        usage: extract_uniques.py [-h] [-p PREFIX] input_biom_fp output_dir mapping_file category_column

Required arguments
^^^^^^^^^^^^^^^^^^

.. cmdoption:: input_biom_fp

    BIOM format file path.

.. cmdoption:: mapping_file

    Mapping file with category information.

.. cmdoption:: category_column

    Column in mapping file specifying the category/condition of all samples.

Optional arguments
^^^^^^^^^^^^^^^^^^

.. cmdoption:: -o OUTPUT_DIR, --output_dir OUTPUT_DIR

    Path to save category unique OTUIDs.

.. cmdoption:: -p PREFIX, --prefix PREFIX

    Provide specific text to prepend the output file names. By default, the 'unique' will be added in front of output filenames.

.. cmdoption:: -r REVERSE, --reverse REVERSE

    Get shared OTUIDs among all unique combinations of groups and write out the results to path provided to this option.

.. cmdoption:: -h, --help

    Show the help message and exit