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Frédéric Boyer
2014-01-31 16:27:17 +00:00
parent 52402e7f8d
commit 3afc23df29
2 changed files with 10 additions and 9 deletions
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src/ecodbtaxstat.py
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#!/usr/local/bin/python #!/usr/local/bin/python
''' '''
:py:mod:`ecodbtaxstat`: Gives taxonomic rank frequency of a given ``ecopcr`` database :py:mod:`ecodbtaxstat`: gives taxonomic rank frequency of a given ``ecopcr`` database
===================================================================================== =====================================================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org> .. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>

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src/ecotaxstat.py
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#!/usr/local/bin/python #!/usr/local/bin/python
''' '''
:py:mod:`ecotaxstat` : Getting the coverage of of an ecoPCR output compared to the original ecoPCR database :py:mod:`ecotaxstat` : getting the coverage of an ecoPCR output compared to the original ecoPCR database
=========================================================================================================== ========================================================================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org> .. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
The :py:mod:`ecotaxstat` command requires two parameters : an ecoPCR formatted database (specified with the `-d` option) The :py:mod:`ecotaxstat` command requires two parameters : an *ecoPCR* formatted database (specified
and an ecoPCR output (ideally computed using the specified ecoPCR database). with the `-d` option, (see :ref:`obiconvert` for a description of the database format) and an ecoPCR
output (ideally computed using the specified ecoPCR database).
The command outputs for every ranks the coverage of the ecoPCR output, that is the fraction of taxids that The command outputs, for every rank, the coverage (Bc) of the ecoPCR output. The coverage (Bc) is the
have a sequence in the database and have also have a sequence in the ecoPCR output file. fraction of *taxids* that have a sequence in the database and have also have a sequence in the ecoPCR
output file.
Optionaly, taxids can be specified to focus the coverage on a smaller part of the taxonomy.
Optionally, *taxids* can be specified to focus the coverage on a smaller part of the taxonomy.
''' '''
from obitools.ecopcr import taxonomy from obitools.ecopcr import taxonomy