def __taxonomy(self, img, genomeIds, outputTaxonomy):
metadata = img.genomeMetadata()
fout = open(outputTaxonomy, "w")
for genomeId in genomeIds:
fout.write("IMG_" + genomeId + "\t")
taxonomy = appendTaxonomyRanks(metadata[genomeId]["taxonomy"])
taxonomy = [x.replace("unclassified", "") for x in taxonomy]
fout.write("; ".join(taxonomy) + "\n")
fout.close()
def __taxonomy(self, img, genomeIds, outputTaxonomy):
metadata = img.genomeMetadata()
fout = open(outputTaxonomy, 'w')
for genomeId in genomeIds:
fout.write('IMG_' + genomeId + '\t')
taxonomy = appendTaxonomyRanks(metadata[genomeId]['taxonomy'])
taxonomy = [x.replace('unclassified', '') for x in taxonomy]
fout.write('; '.join(taxonomy) + '\n')
fout.close()
def testAppendTaxonomyRanks(self):
"""Verify computation of base count on mixed-case sequence."""
r = appendTaxonomyRanks(['k', 'p', 'c'], ranks=3)
self.assertEqual(r, ['k__k', 'p__p', 'c__c'])