Commit 1d461b93 by Aurélie Bonin

--no commit message

parent 0e231b42
......@@ -43,6 +43,28 @@ Otherwise,
scientific taxon name, the sequence record is stored in the file specified by the
``-u`` option.
*Example*
.. code-block:: bash
> obiaddtaxids -T species_name -g genus_identified.fasta \\
-u unidentified.fasta -d my_ecopcr_database \\
my_sequences.fasta > identified.fasta
Tries to match the value associated with the ``species_name`` key of each sequence record
from the ``my_sequences.fasta`` file with a taxon name from the ecopcr database ``my_ecopcr_database``.
- If there is an exact match, the sequence record is stored in the ``identified.fasta`` file.
- If not and the ``species_name`` value is composed of two words, :py:mod:`obiaddtaxids`:
considers the first word as a genus name and tries to find it into the taxonomic database.
- If a genus is found, the sequence record is stored in the ``genus_identified.fasta``
file.
- Otherwise the sequence record is stored in the ``unidentified.fasta`` file.
'''
......
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