import os
import sys
import argparse
import taxon
import re
ffdir = 'flatfiles' # the location of our genbank flatfiles
blastpf = 'phage_genes.nr.blastp'
genome = {} # hash with protein IDs as key and genome as value
numprots = {} # hash with genome ID as key and number of proteins as value
taxondir = "/home2/db/taxonomy/current/"
sys.stderr.write("Reading taxonomy\n")
taxa = taxon.read_nodes(directory=taxondir)
names, blastname = taxon.read_names(directory=taxondir)
sys.stderr.write("Read taxonomy\n")
# first read how many proteins there are per genome
# and create a list of protein ids->genomes.
# Note also throw a fatal error if IDs duplicated because I forgot to check this earlier!
for f in os.listdir(ffdir):
with open(os.path.join(ffdir, f), 'r') as fin:
for l in fin:
p = l.strip().split("\t")
if p[5] in genome:
sys.stderr.write(
"FATAL AND BUGGER: {} was found in {} and {}\n".format(
p[5], genome[p[0]], p[0]))
genome[p[5]] = p[0]
numprots[p[0]] = numprots.get(p[0], 0) + 1
import sys
import argparse
import taxon
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Append taxonomy to the patric metadata file. This adds it at column 67")
parser.add_argument('-f', help='patric metadata file', required=True)
parser.add_argument('-o', help='output file', required=True)
parser.add_argument('-t', help='taxonomy directory (default=/home2/db/taxonomy/current/)',
default='/home2/db/taxonomy/current/')
parser.add_argument('-v', help='verbose output', action="store_true")
args = parser.parse_args()
sys.stderr.write("Reading taxonomy\n")
taxa = taxon.read_nodes(directory=args.t)
names, blastname = taxon.read_names(directory=args.t)
divs = taxon.read_divisions(directory=args.t)
sys.stderr.write("Read taxonomy\n")
want = ['superkingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']
with open(args.o, 'w', encoding='utf-8') as out:
with open(args.f, 'r', encoding='utf-8') as f:
for l in f:
p = l.strip().split("\t")
while (len(p) <= 68):
p.append("")
if l.startswith("genome_id"):
out.write("{}\t{}\n".format(l.strip(), "\t".join(want)))
continue
import sys
import argparse
import taxon
__author__ = 'Rob Edwards'
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Parse a tsv file and add taxonomy')
parser.add_argument('-f', help='tab seperated values', required=True)
args = parser.parse_args()
want = ['superkingdom', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']
sys.stderr.write("Reading databases\n")
taxa = taxon.read_nodes()
names, blastname = taxon.read_names()
sys.stderr.write("Done\n")
with open(args.f, 'r') as f:
for l in f:
if l.startswith("#"):
print("{}\t".format(l.strip()) + "\t".join(want))
continue
p = l.strip().split("\t")
m = ["" for w in want]
i = p[2]
if i in taxa:
while taxa[i].parent != '1' and i != '1':
if taxa[i].rank in want:
m[want.index(taxa[i].rank)] = names[i].name
i = taxa[i].parent
__author__ = 'Rob Edwards'
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description='Parse a tsv file and add taxonomy')
parser.add_argument('-f', help='tab seperated values', required=True)
args = parser.parse_args()
want = [
'superkingdom', 'kingdom', 'phylum', 'class', 'order', 'family',
'genus', 'species'
]
sys.stderr.write("Reading databases\n")
taxa = taxon.read_nodes()
names, blastname = taxon.read_names()
sys.stderr.write("Done\n")
with open(args.f, 'r') as f:
for l in f:
if l.startswith("#"):
print("{}\t".format(l.strip()) + "\t".join(want))
continue
p = l.strip().split("\t")
m = ["" for w in want]
i = p[2]
if i in taxa:
while taxa[i].parent != '1' and i != '1':
if taxa[i].rank in want:
m[want.index(taxa[i].rank)] = names[i].name
i = taxa[i].parent
import taxon
import re
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Read a blast file and create a tuple of [query / kingdom / phylum / genus / species]")
parser.add_argument('-f', help='blast file(s). Note this must have taxids as column 14. You may specify more than one file', nargs='+')
parser.add_argument('-t', help='taxonomy directory (default=/home2/db/taxonomy/current/)', default='/home2/db/taxonomy/current/')
parser.add_argument('-v', help='verbose output', action="store_true")
args = parser.parse_args()
want = ['superkingdom', 'phylum', 'genus', 'species']
if args.v:
sys.stderr.write("Reading taxonomy\n")
taxa=taxon.read_nodes(directory=args.t)
names,blastname = taxon.read_names(directory=args.t)
if args.v:
sys.stderr.write("Read taxonomy\n")
for blastf in args.f:
if args.v:
sys.stderr.write("Reading {}\n".format(blastf))
with open(blastf, 'r') as fin:
for l in fin:
p=l.strip().split("\t")
for tid in p[14].split(";"):
level = {}
results = [p[0], tid]
while tid != '0' and tid != '1' and tid in taxa and taxa[tid].parent != '1':