.. automodule:: obiaddtaxids

    :py:mod:`obiaddtaxids` specific options
    --------------------------------------- 

    .. cmdoption::  -f <FORMAT>, --format=<FORMAT>

                        Format of the sequence file. Possibilities : ``raw``, ``UNITE`` or ``SILVA`` 
                        (default: ``raw``).
                        
    .. cmdoption::  -k <KEYNAME>, --key-name=<KEYNAME>

                        Key of the attribute containing the taxon name in sequence files in ``raw`` format. 
                        Default: the taxon name is :doc:`the id of the sequence record<../fasta>`. The taxon name 
                        MUST have ``_`` between the words of the name when it's the *id*, and CAN be in this format 
                        when it's in an attribute.

    .. cmdoption::  -a <ANCESTOR>, --restricting_ancestor=<ANCESTOR>

                        Can be a word or a number (taxid). Enables to restrict the search of taxids under a 
                        specified ancestor. If it is a word, it is the attribute key associated with the 
                        ancestor's taxid in each sequence record (it can be different for each sequence record). 
                        If it is a number, it is the taxid of the ancestor (in which case it is the same for all 
                        the sequence records).

    .. cmdoption::  -g <FILENAME>, --genus_found=<FILENAME>

                        File used to store sequences with a match found for the genus (not with UNITE databases).
                        
    .. cmdoption::  -s <FILENAME>, --dirty=<FILENAME>

                        File used to store sequences with a match found for one of the words from the taxon name 
                        searched (not with UNITE databases).

    .. cmdoption::  -u <FILENAME>, --unidentified=<FILENAME>

                        File used to store sequences with no match found.

    .. include:: ../optionsSet/taxonomyDB.txt

    .. include:: ../optionsSet/defaultoptions.txt
