def condense(args):
"""
%prog condense OM.bed
Merge split alignments in OM bed.
"""
from itertools import groupby
from jcvi.assembly.patch import merge_ranges
p = OptionParser(condense.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(bedfile,) = args
bed = Bed(bedfile, sorted=False)
key = lambda x: (x.seqid, x.start, x.end)
for k, sb in groupby(bed, key=key):
sb = list(sb)
b = sb[0]
chr, start, end, strand = merge_ranges(sb)
id = "{0}:{1}-{2}".format(chr, start, end)
b.accn = id
print(b)
def condense(args):
"""
%prog condense OM.bed
Merge split alignments in OM bed.
"""
from itertools import groupby
from jcvi.assembly.patch import merge_ranges
p = OptionParser(condense.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bedfile, = args
bed = Bed(bedfile, sorted=False)
key = lambda x: (x.seqid, x.start, x.end)
for k, sb in groupby(bed, key=key):
sb = list(sb)
b = sb[0]
chr, start, end, strand = merge_ranges(sb)
id = "{0}:{1}-{2}".format(chr, start, end)
b.accn = id
print b