def pairs(args):
"""
See __doc__ for set_options_pairs().
"""
from jcvi.formats.blast import report_pairs, set_options_pairs
p = set_options_pairs()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bedfile, = args
basename = bedfile.split(".")[0]
insertsfile = ".".join((basename, "inserts"))
sortedbedfile = op.basename(bedfile).rsplit(".", 1)[0] + ".sorted.bed"
if need_update(bedfile, sortedbedfile):
bedfile = sort([bedfile, "--accn"])
else:
bedfile = sortedbedfile
fp = open(bedfile)
data = [BedLine(row) for i, row in enumerate(fp) if i < opts.nrows]
ascii = not opts.pdf
return bedfile, report_pairs(data, opts.cutoff, opts.mateorientation,
pairsfile=opts.pairsfile, insertsfile=insertsfile,
rclip=opts.rclip, ascii=ascii, bins=opts.bins,
distmode=opts.distmode)
def pairs(args):
"""
See __doc__ for set_options_pairs().
"""
import jcvi.formats.bed
p = set_options_pairs()
opts, targs = p.parse_args(args)
if len(targs) != 1:
sys.exit(not p.print_help())
frgscffile, = targs
bedfile = bed([frgscffile])
args[args.index(frgscffile)] = bedfile
return jcvi.formats.bed.pairs(args)
def pairs(args):
"""
See __doc__ for set_options_pairs().
"""
import jcvi.formats.bed
p = set_options_pairs()
opts, targs = p.parse_args(args)
if len(targs) != 1:
sys.exit(not p.print_help())
casfile, = targs
bedfile = bed([casfile])
args[args.index(casfile)] = bedfile
return jcvi.formats.bed.pairs(args)
def pairs(args):
"""
See __doc__ for set_options_pairs().
"""
from jcvi.formats.blast import report_pairs, set_options_pairs
p = set_options_pairs()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bedfile, = args
basename = bedfile.split(".")[0]
insertsfile = ".".join((basename, "inserts"))
sortedbedfile = op.basename(bedfile).rsplit(".", 1)[0] + ".sorted.bed"
if need_update(bedfile, sortedbedfile):
bedfile = sort([bedfile, "--accn"])
else:
bedfile = sortedbedfile
fp = open(bedfile)
data = [BedLine(row) for i, row in enumerate(fp) if i < opts.nrows]
ascii = not opts.pdf
return bedfile, report_pairs(data,
opts.cutoff,
opts.mateorientation,
pairsfile=opts.pairsfile,
insertsfile=insertsfile,
rclip=opts.rclip,
ascii=ascii,
bins=opts.bins,
distmode=opts.distmode)
