Commit a0424519 by Frédéric Boyer

[MOD] documentation for ecotaxstat

parent d6e80544
:py:mod:`ecotaxstat` : Getting the coverage of of an ecoPCR output compared to the original ecoPCR database
.. codeauthor:: Eric Coissac <>
The :py:mod:`ecotaxstat` command requires two parameters : an ecoPCR formatted database (specified with the
``-d``option) and an ecoPCR output (ideally computing on the specified ecoPCR database).
The command outputs for every ranks the coverage of the ecoPCR output, that is the 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.
from obitools.ecopcr import taxonomy
from obitools.ecopcr import sequence
......@@ -34,7 +50,7 @@ if __name__=='__main__':
(options, entries) = optionParser()
if (options.db is None):
print sys.stderr, "-d option is required"
print>>sys.stderr, "-d option is required"
tax = taxonomy.EcoTaxonomyDB(options.db)
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