Commit 27b2ec45 by Celine Mercier

changed the location of the obiaddtaxids example

parent 37f9963c
.. automodule:: obiaddtaxids
*Example:*
.. code-block:: bash
> obiaddtaxids -T species_name -g genus_identified.fasta -u unidentified.fasta -d my_ecopcr_database_prefix my_sequences.fasta > identified.fasta
Tries to match the value associated with the ``species_name`` key of each sequence record from ``my_sequences.fasta``
with a taxon name from the ecopcr database ``my_ecopcr_database_prefix``. If there is an exact match, the sequence
record is printed in ``identified.fasta``. If not and the ``species_name`` value is composed of two words, tries to
match the first word with a taxon name from the ecopcr database. If there is a match, the sequence record is printed in
``genus_identified.fasta``. If the sequence record was printed in neither ``identified.fasta`` nor in ``genus_identified``,
it is printed in ``unidentified.fasta``.
:py:mod:`obiaddtaxids` specific options
---------------------------------------
......@@ -39,3 +53,4 @@
.. include:: ../optionsSet/taxonomyDB.txt
.. include:: ../optionsSet/defaultoptions.txt
\ No newline at end of file
......@@ -28,22 +28,9 @@ and will print it with the associated taxid if a match is found.
If the ``-u`` option is set and a sequence was printed neither in the output, the ``-g`` file nor the ``-s`` file, it is printed in
the file set by the ``-u`` option.
*Example:*
.. code-block:: bash
> obiaddtaxids -T species_name -g genus_identified.fasta -u unidentified.fasta -d my_ecopcr_database_prefix my_sequences.fasta > identified.fasta
Tries to match the value associated with the ``species_name`` key of each sequence record from ``my_sequences.fasta``
with a taxon name from the ecopcr database ``my_ecopcr_database_prefix``. If there is an exact match, the sequence
record is printed in ``identified.fasta``. If not and the ``species_name`` value is composed of two words, tries to
match the first word with a taxon name from the ecopcr database. If there is a match, the sequence record is printed in
``genus_identified.fasta``. If the sequence record was printed in neither ``identified.fasta`` nor in ``genus_identified``,
it is printed in ``unidentified.fasta``.
'''
import sys
from obitools.fasta import fastaIterator,formatFasta
......
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