# only return genus and species ... dump everything after the first two words and remove dots
if species:
return species.split()[0] + " " + species.split()[1]
else: # return None if we didn't find the accession in Uniprot, or there was no species field
return None
for s in seqs:
try:
# take "Q9Y0V5_CIOIN" from "Q9Y0V5_CIOIN blabla bla" & retrieve Uniprot record
uniprot_id = s.description.split()[0]
species = uniprotGetSpecies(uniprot_id)
# If nothing was returned from Uniprot the first time
# take only "Q9Y0V5" from "Q9Y0V5_CIOIN blabla bla" and try again
if not species:
uniprot_id = s.description.split()[0].split("_")[0]
species = uniprotGetSpecies(uniprot_id)
except IndexError: # no [genus species] in the description for this sequence
continue
#print "Species: ", species
lineage_code = server.getLineageCode(species, kingdoms=KINGDOMS)
if lineage_code == None:
lineage_code = server.getLineageCode(species, kingdoms=SUPERKINGDOMS)
if tag_end:
print ">%s |||%s" % (s.description, lineage_code)
else:
print ">tax|%s|%s" % (lineage_code, s.description)
print s.seq.tostring()
fh.close()
else:
server = SOAPpy.SOAPProxy("http://localhost:8999/")
#def get_lineage_code(species, kingdoms=KINGDOMS):
# lineage = server.getLineage(species)
# for l in lineage:
# for n in l:
# #print "----------------"
# for x in n:
# if x in kingdoms:
# return kingdoms[x]
# return None
for s in seqs:
try:
species = s.description.split("[")[1].split("]")[0].strip()
except IndexError: # no [genus species] in the description for this sequence
continue
#print "Species: ", species
lineage_code = server.getLineageCode(species, kingdoms=KINGDOMS)
if lineage_code == None:
lineage_code = server.getLineageCode(species, kingdoms=SUPERKINGDOMS)
if tag_end:
print ">%s |||%s" % (s.description, lineage_code)
else:
print ">tax|%s|%s" % (lineage_code, s.description)
print s.seq.tostring()
fh.close()
