def _getNodeHitFunction(hit, taxMap):
newHit = getNodeFromHit(hit, taxMap)
if newHit is None:
return hit
else:
return newHit
def main():
usage = '%prog [OPTIONS] TAXDUMP_PATH'
description = 'reduce full RefSea catalog (from STDIN) to acc->taxid map using TAXDUMP to verify taxids'
parser = OptionParser(usage, description=description)
parser.add_option(
"-g",
"--genomic",
default=False,
action="store_true",
help="output genoic accessions instead of proteins")
parser.add_option(
"-v",
"--verbose",
action="count",
dest="verbose",
default=1,
help="Print log messages. Use twice for debugging")
parser.add_option(
"-q",
'--quiet',
dest='verbose',
action="store_const",
const=0,
help="Suppress warnings. Only print fatal messages")
parser.add_option(
"-A",
"--about",
action="store_true",
dest="about",
default=False,
help="Print description")
(options, args) = parser.parse_args()
if options.about:
print description
exit(0)
# check args
if options.verbose == 0:
loglevel = logging.ERROR
elif options.verbose == 1:
loglevel = logging.WARN
elif options.verbose == 2:
loglevel = logging.INFO
elif options.verbose >= 3:
loglevel = logging.DEBUG
logging.basicConfig(stream=sys.stderr, level=loglevel)
logging.info("Log level set to %r(%d)" % (loglevel, options.verbose))
if len(args) != 1:
parser.error("Please supply TAXDUMP path in command line")
# parse catalog
accToOrg = {}
accRE = re.compile(r'\b([A-Z]{2}_[A-Z]*\d+)(\.\b)?\b')
protRE = re.compile(r'^([ANXWYZ]P_[A-Z]*\d+)$')
logging.info("reading catalog from STDIN")
for line in sys.stdin:
cells = line.rstrip('\r\n').split('\t')
(taxid, name, acc) = cells[0:3]
try:
taxid = int(taxid)
except:
pass
logging.debug(acc)
acc = accRE.match(acc).group(1)
logging.debug("'%s'" % acc)
m = protRE.match(acc)
if (m == None) == options.genomic:
# will match if acc matches exp and genomic is false OR
# if acc doesn't match and genomic is true
accToOrg[acc] = (taxid, name)
logging.debug("USing acc: %s" % (acc))
else:
logging.debug("Skipping acc: %s" % (acc))
# load taxonomy
logging.info("loading taxonomy from %s" % (args[0]))
taxonomy = readTaxonomy(args[0], namesMap=True)
# print table
changes = 0
for (acc, (taxid, name)) in accToOrg.iteritems():
if taxid not in taxonomy.idMap:
node = getNodeFromHit(name, taxonomy.nameMap)
logging.debug("Changing %s to %s" % (taxid, node.id))
taxid = node.id
changes += 1
print '\t'.join([acc, str(taxid)])
logging.info("Changed %d taxon ids" % changes)
def _getNodeHitFunction(hit, taxMap):
newHit = getNodeFromHit(hit, taxMap)
if newHit is None:
return hit
else:
return newHit
def main():
usage = '%prog [OPTIONS] TAXDUMP_PATH'
description = 'reduce full RefSea catalog (from STDIN) to acc->taxid map using TAXDUMP to verify taxids'
parser = OptionParser(usage, description=description)
parser.add_option("-g",
"--genomic",
default=False,
action="store_true",
help="output genoic accessions instead of proteins")
parser.add_option("-v",
"--verbose",
action="count",
dest="verbose",
default=1,
help="Print log messages. Use twice for debugging")
parser.add_option("-q",
'--quiet',
dest='verbose',
action="store_const",
const=0,
help="Suppress warnings. Only print fatal messages")
parser.add_option("-A",
"--about",
action="store_true",
dest="about",
default=False,
help="Print description")
(options, args) = parser.parse_args()
if options.about:
print(description)
exit(0)
# check args
if options.verbose == 0:
loglevel = logging.ERROR
elif options.verbose == 1:
loglevel = logging.WARN
elif options.verbose == 2:
loglevel = logging.INFO
elif options.verbose >= 3:
loglevel = logging.DEBUG
logging.basicConfig(stream=sys.stderr, level=loglevel)
logging.info("Log level set to %r(%d)" % (loglevel, options.verbose))
if len(args) != 1:
parser.error("Please supply TAXDUMP path in command line")
# parse catalog
accToOrg = {}
accRE = re.compile(r'\b([A-Z]{2}_[A-Z]*\d+)(\.\b)?\b')
protRE = re.compile(r'^([ANXWYZ]P_[A-Z]*\d+)$')
logging.info("reading catalog from STDIN")
for line in sys.stdin:
cells = line.rstrip('\r\n').split('\t')
(taxid, name, acc) = cells[0:3]
try:
taxid = int(taxid)
except:
pass
logging.debug(acc)
acc = accRE.match(acc).group(1)
logging.debug("'%s'" % acc)
m = protRE.match(acc)
if (m == None) == options.genomic:
# will match if acc matches exp and genomic is false OR
# if acc doesn't match and genomic is true
accToOrg[acc] = (taxid, name)
logging.debug("USing acc: %s" % (acc))
else:
logging.debug("Skipping acc: %s" % (acc))
# load taxonomy
logging.info("loading taxonomy from %s" % (args[0]))
taxonomy = readTaxonomy(args[0], namesMap=True)
# print table
changes = 0
for (acc, (taxid, name)) in accToOrg.iteritems():
if taxid not in taxonomy.idMap:
node = getNodeFromHit(name, taxonomy.nameMap)
logging.debug("Changing %s to %s" % (taxid, node.id))
taxid = node.id
changes += 1
print('\t'.join([acc, str(taxid)]))
logging.info("Changed %d taxon ids" % changes)
