def __init__(self):
sys.stderr.write("Parsing the taxonomy files\n")
self.taxa = taxon.readNodes()
self.names, self.blastname, self.genbankname, self.synonym = taxon.extendedNames(
)
self.divs = taxon.readDivisions()
sys.stderr.write("Done parsing the taxonomy\n")
self.wanted = [
'species', 'genus', 'family', 'order', 'class', 'phylum',
'superkingdom'
]
self.taxonomy = {}
self.nc2tax = {}
try:
inputF = sys.argv[1]
except:
sys.exit(
sys.argv[0] +
" <file of taxon ids separated with tabs (phage in first column)>")
wanted = [
'species', 'genus', 'family', 'order', 'class', 'phylum', 'superkingdom'
]
match = {w: 0 for w in wanted}
mismatch = {w: 0 for w in wanted}
taxa = taxon.readNodes()
names, blastname, genbankname, synonym = taxon.extendedNames()
divs = taxon.readDivisions()
with open(inputF, 'r') as inf:
for line in inf:
line = line.strip()
hosts = line.split('\t')
phage = hosts.pop(0)
taxonomy = {}
taxonomy[phage] = {}
for h in hosts:
taxonomy[h] = {}
if phage not in taxa:
sys.stderr.write("SKIPPED: Phage " + str(phage) +
" not found in the taxonomy\n")
continue
import sys
import taxon
## run this as a script
if __name__ == "__main__":
ids=['1211997']
if len(sys.argv) == 1:
print "Supply your own id for the tree. Here is an example"
else:
ids=sys.argv[1:]
taxa = taxon.readNodes()
names,blastname = taxon.readNames()
divs = taxon.readDivisions()
for i in ids:
c=0
if i not in taxa:
sys.stderr.write("Error: ID " + str(i) + " was not found in the taxonomy filei\n")
sys.exit(0)
while taxa[i].parent != '1' and i != '1':
#print " " * c, taxa[i].taxid, "name:", names[i].name, "rank:", taxa[i].rank, "div:", taxa[i].division, "code:", divs[taxa[i].division].code
bn=names[i].name
if i in blastname:
bn=blastname[i].name
print taxa[i].taxid, "name:", names[i].name, "blast name", bn, "rank:", taxa[i].rank, "parent: ", taxa[i].parent
i=taxa[i].parent
c+=1
print