Commit 8135683f by Celine Mercier

obiaddtaxids doc

parent 6854a0ab
.. automodule:: obiaddtaxids
:py:mod:`obiaddtaxids` specific options
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.. cmdoption:: -p, --pouic
Pouic
\ No newline at end of file
: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
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