def __init__(self, title=None):
if title:
self.title = title
else:
self.title = []
self.result = []
self._keggdb = dbutils.keggdb()
def __init__(self, title=None):
if title:
self.title = title
else:
self.title = []
self.result = []
self._keggdb = dbutils.keggdb()
def dist_from_annot_file(handle):
dist = Dist()
mykeggdb = dbutils.keggdb()
for l in handle:
if l[0] == '#':
continue
query, kos = parse_annot(l)
if not kos: continue
for ko in kos:
paths = mykeggdb.get_ko3s(ko)
for path in paths:
dist[path] = query
return dist
def dist_from_annot_file(handle):
dist = Dist()
mykeggdb = dbutils.keggdb()
for l in handle:
if l[0] == "#":
continue
query, kos = parse_annot(l)
if not kos:
continue
for ko in kos:
paths = mykeggdb.get_ko3s(ko)
for path in paths:
dist[path] = query
return dist
def arg2dist(arg):
""" get dist dict in term of arg, abbrev for genome or used defined annot
"""
kobasrc = config.getrc()
if len(arg) == 3:
keggdb = dbutils.keggdb()
distfile = os.path.join(kobasrc["kobas_home"], "gene_dist",
keggdb.get_species_name(arg.lower()))
dist_dict = discover.dist_from_distfile(open(distfile))
else:
if not os.access(arg, os.F_OK):
print "File: %s not exist" % arg
sys.exit(0)
dist_dict = discover.dist_from_annot_file(open(arg, 'r'))
dist_size = dist_dict.size()
return (dist_dict, dist_size)
def arg2dist(arg):
""" get dist dict in term of arg, abbrev for genome or used defined annot
"""
kobasrc = config.getrc()
if len(arg) == 3:
keggdb = dbutils.keggdb()
distfile = os.path.join(
kobasrc["kobas_home"], "gene_dist",
keggdb.get_species_name(arg.lower()))
dist_dict = discover.dist_from_distfile(open(distfile))
else:
if not os.access(arg, os.F_OK):
print "File: %s not exist" % arg
sys.exit(0)
dist_dict = discover.dist_from_annot_file(open(arg, 'r'))
dist_size = dist_dict.size()
return (dist_dict, dist_size)
def annot2dist(handle):
""" convert annotation to term distribution, besides total size
"""
dist_dict = {}
dist_size = 0
mykeggdb = dbutils.keggdb()
for l in handle:
terms = []
if l[0] == "#":
continue
query, kos = parse_annot(l)
if kos:
dist_size += 1
[terms.extend(mykeggdb.get_ko3s(koid)) for koid in kos]
term_freq(dist_dict, [(term, 1) for term in terms])
return (dist_dict, dist_size)
def annot2dist(handle):
""" convert annotation to term distribution, besides total size
"""
dist_dict = {}
dist_size = 0
mykeggdb = dbutils.keggdb()
for l in handle:
terms = []
if l[0] == '#':
continue
query, kos = parse_annot(l)
if kos:
dist_size += 1
[terms.extend(mykeggdb.get_ko3s(koid)) for koid in kos]
term_freq(dist_dict, [(term, 1) for term in terms])
return (dist_dict, dist_size)
opt_parser,opt,args = config_option()
if len(args) != 1:
opt_parser.print_help()
sys.exit(1)
# Blast environment configuration
kobasrc = config.getrc()
# Integrate command line switches into environments
if opt.rank:
kobasrc["rank"] = opt.rank
if opt.evalue:
kobasrc["evalue"] = opt.evalue
keggdb = dbutils.keggdb(kobasrc['kobasdb'])
if opt.intype == "fasta":
# verify fasta file
try:
try:
f = open(args[0])
fasta.verify(f)
finally:
f.close()
except exception.FastaIOError, msg:
exception.error(msg)
sys.exit(1)
annotator = annot.Annotator(
reader = annot.BlastProgReader(
kobasrc['blast'], opt.blast_prog, kobasrc['blastdb'], args[0],
opt_parser, opt, args = config_option()
if len(args) != 1:
opt_parser.print_help()
sys.exit(1)
# Blast environment configuration
kobasrc = config.getrc()
# Integrate command line switches into environments
if opt.rank:
kobasrc["rank"] = opt.rank
if opt.evalue:
kobasrc["evalue"] = opt.evalue
keggdb = dbutils.keggdb(kobasrc['kobasdb'])
if opt.intype == "fasta":
# verify fasta file
try:
try:
f = open(args[0])
fasta.verify(f)
finally:
f.close()
except exception.FastaIOError, msg:
exception.error(msg)
sys.exit(1)
annotator = annot.Annotator(
reader=annot.BlastProgReader(kobasrc['blast'],
opt.blast_prog,
def setUp(self):
self._keggdb = dbutils.keggdb()
global similarity
return record.get_similarity() >= similarity
def usage():
print >> sys.stderr, __doc__
sys.exit(1)
if __name__ == "__main__":
opts, args = getopt.getopt(sys.argv[1:], 'e:hi:o:r:s:t:')
if len(args) != 1:
usage()
f = open(args[0], 'r')
annot_iter = annot.Iterator(f)
keggdb = dbutils.keggdb()
# kobasrc = config.getrc()
# evalue = float(kobasrc['evalue'])
# rank = int(kobasrc['rank'])
output = 't'
for o, a in opts:
if o == '-e':
evalue = float(a)
elif o == '-i':
similarity = float(a)
elif o == '-r':
rank = int(a)
elif o == '-o':
if a == 'o': output = 'o'
def usage():
print >> sys.stderr, __doc__
sys.exit(1)
if __name__ == "__main__":
opts, args = getopt.getopt(sys.argv[1:], 'e:hi:o:r:s:t:')
if len(args) != 1:
usage()
f = open(args[0], 'r')
annot_iter = annot.Iterator(f)
keggdb = dbutils.keggdb()
# kobasrc = config.getrc()
# evalue = float(kobasrc['evalue'])
# rank = int(kobasrc['rank'])
output = 't'
for o, a in opts:
if o == '-e':
evalue = float(a)
elif o == '-i':
similarity = float(a)
elif o == '-r':
rank = int(a)
elif o == '-o':
if a == 'o': output = 'o'
def setUp(self):
self._keggdb = dbutils.keggdb()
