Commit 646341b5 by Frédéric Boyer

[ADD] Documentation for ecoDBTaxStat

parent 03faa946
.. automodule:: ecoDBTaxStat
:py:mod:`ecoDBTaxStat` specific options
------------------------------------
.. cmdoption:: --rank=<TAXONOMIC_RANK>
The taxonomic rank at which frequencies have to be computed.
Possible values are :
- class
- family
- forma
- genus
- infraclass
- infraorder
- kingdom
- no rank
- order
- parvorder
- phylum
- species [default]
- species group
- species subgroup
- subclass
- subfamily
- subgenus
- subkingdom
- suborder
- subphylum
- subspecies
- subtribe
- superclass
- superfamily
- superkingdom
- superorder
- superphylum
- tribe
- varietas
\ No newline at end of file
......@@ -7,7 +7,7 @@ from obitools.ecopcr import EcoPCRFile
from obitools.options import getOptionManager
from obitools.ecopcr.options import loadTaxonomyDatabase
import sys
def addTaxonomyOptions(optionManager):
......@@ -29,11 +29,14 @@ def addTaxonomyOptions(optionManager):
if __name__=='__main__':
optionParser = getOptionManager([addTaxonomyOptions],
entryIterator=EcoPCRFile
)
entryIterator=EcoPCRFile)
(options, entries) = optionParser()
if (options.db is None)
print sys.stderr, "-d option is required"
sys.exit(1)
tax = taxonomy.EcoTaxonomyDB(options.db)
seqd= sequence.EcoPCRDBSequenceIterator(options.db,taxonomy=tax)
......
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