def eject(args):
"""
%prog eject candidates.bed chr.fasta
Eject scaffolds from assembly, using the range identified by closest().
"""
p = OptionParser(eject.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
candidates, chrfasta = args
sizesfile = Sizes(chrfasta).filename
cbedfile = complementBed(candidates, sizesfile)
cbed = Bed(cbedfile)
for b in cbed:
b.accn = b.seqid
b.score = 1000
b.strand = "+"
cbed.print_to_file()
def eject(args):
"""
%prog eject candidates.bed chr.fasta
Eject scaffolds from assembly, using the range identified by closest().
"""
p = OptionParser(eject.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
candidates, chrfasta = args
sizesfile = Sizes(chrfasta).filename
cbedfile = complementBed(candidates, sizesfile)
cbed = Bed(cbedfile)
for b in cbed:
b.accn = b.seqid
b.score = 1000
b.strand = '+'
cbed.print_to_file()