def publocus(args):
"""
%prog publocus idsfile > idsfiles.publocus
Given a list of model identifiers, convert each into a GenBank approved
pub_locus.
Example output:
Medtr1g007020.1 MTR_1g007020
Medtr1g007030.1 MTR_1g007030
Medtr1g007060.1 MTR_1g007060A
Medtr1g007060.2 MTR_1g007060B
"""
from jcvi.utils.cbook import AutoVivification
p = OptionParser(publocus.__doc__)
p.add_option("--locus_tag",
default="MTR_",
help="GenBank locus tag [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
locus_tag = opts.locus_tag
index = AutoVivification()
idsfile, = args
fp = must_open(idsfile)
for row in fp:
locus, chrom, sep, rank, iso = atg_name(
row, retval="locus,chr,sep,rank,iso")
if None in (locus, chrom, sep, rank, iso):
logging.warning(
"{0} is not a valid gene model identifier".format(row))
continue
if locus not in index.keys():
pub_locus = gene_name(chrom, rank, prefix=locus_tag, sep=sep)
index[locus]['pub_locus'] = pub_locus
index[locus]['isos'] = set()
index[locus]['isos'].add(int(iso))
for locus in index:
pub_locus = index[locus]['pub_locus']
Index[locus]['isos'] = sorted(index[locus]['isos'])
if len(index[locus]['isos']) > 1:
new = [chr(n + 64) for n in index[locus]['isos'] if n < 27]
for i, ni in zip(index[locus]['isos'], new):
print "\t".join(x for x in ("{0}.{1}".format(locus, i), \
"{0}{1}".format(pub_locus, ni)))
else:
print "\t".join(x for x in ("{0}.{1}".format(locus, index[locus]['isos'][0]), \
pub_locus))
def publocus(args):
"""
%prog publocus idsfile > idsfiles.publocus
Given a list of model identifiers, convert each into a GenBank approved
pub_locus.
Example output:
Medtr1g007020.1 MTR_1g007020
Medtr1g007030.1 MTR_1g007030
Medtr1g007060.1 MTR_1g007060A
Medtr1g007060.2 MTR_1g007060B
"""
from jcvi.utils.cbook import AutoVivification
p = OptionParser(publocus.__doc__)
p.add_option("--locus_tag", default="MTR_",
help="GenBank locus tag [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
locus_tag = opts.locus_tag
index = AutoVivification()
idsfile, = args
fp = must_open(idsfile)
for row in fp:
locus, chrom, sep, rank, iso = atg_name(row, retval="locus,chr,sep,rank,iso")
if None in (locus, chrom, sep, rank, iso):
logging.warning("{0} is not a valid gene model identifier".format(row))
continue
if locus not in index.keys():
pub_locus = gene_name(chrom, rank, prefix=locus_tag, sep=sep)
index[locus]['pub_locus'] = pub_locus
index[locus]['isos'] = set()
index[locus]['isos'].add(int(iso))
for locus in index:
pub_locus = index[locus]['pub_locus']
Index[locus]['isos'] = sorted(index[locus]['isos'])
if len(index[locus]['isos']) > 1:
new = [chr(n+64) for n in index[locus]['isos'] if n < 27]
for i, ni in zip(index[locus]['isos'], new):
print "\t".join(x for x in ("{0}.{1}".format(locus, i), \
"{0}{1}".format(pub_locus, ni)))
else:
print "\t".join(x for x in ("{0}.{1}".format(locus, index[locus]['isos'][0]), \
pub_locus))
