=============
prune_otus.py
=============

Parse the OTU-sequence data in two steps. First remove any OTUs that occur in
less than a user-defined percent of samples (default 5%). Second, remove any
OTUs that make up less than a user-defined percentage of the overall sequences
(default 0.01%)

.. code-block:: bash

        usage: prune_otus.py [-h] -i SEQS_OTUS_FN -t ID_TO_TAXONOMY_FN [-p PERCENT_OF_SAMPLES] [-s PERCENT_OF_SEQUENCES] [-l {k,p,c,o,f,g,s}] [-o OUTPUT_PRUNED_OTUS_FN] [--output_removed_otus_fn OUTPUT_REMOVED_OTUS_FN] [-v]

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

.. cmdoption:: -i SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN

    The output from the pick OTUs step, e.g. seqs_otus.txt

.. cmdoption:: -t ID_TO_TAXONOMY_FN, --id_to_taxonomy_fn ID_TO_TAXONOMY_FN

    Path to tab-delimited file mapping sequences to assigned taxonomy.

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

.. cmdoption:: -p PERCENT_OF_SAMPLES, --percent_of_samples PERCENT_OF_SAMPLES

    OTUs that occur in less than this percent of samples
    will be removed. Default is 5 percent.

.. cmdoption:: -s PERCENT_OF_SEQUENCES, --percent_of_sequences PERCENT_OF_SEQUENCES

    OTUs that occur in less than this percent of total
    sequences will be removed. Default is 0.01 percent.

.. cmdoption:: -l {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s}

    Set the phylogenetic level at which to join OTUs for
    consideration in pruning. Default is 'g'(group).

.. cmdoption:: -o OUTPUT_PRUNED_OTUS_FN, --output_pruned_otus_fn OUTPUT_PRUNED_OTUS_FN

    The main output file that will contain the remaining
    OTUs and sequence IDs.

.. cmdoption:: --output_removed_otus_fn OUTPUT_REMOVED_OTUS_FN

    The file to write out the set of OTUs that were removed by the filter.

.. cmdoption:: -h, --help

    Show the help message and exit

.. cmdoption:: -v, --verbose

    Print detailed information about script operation.