def bed(args):
"""
%prog bed blastfile
Print out bed file based on coordinates in BLAST report. By default, write
out subject positions. Use --swap to write query positions.
"""
from jcvi.formats.bed import sort as bed_sort
p = OptionParser(bed.__doc__)
p.add_option("--swap", default=False, action="store_true",
help="Write query positions [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(p.print_help())
blastfile, = args
swap = opts.swap
fp = must_open(blastfile)
bedfile = blastfile.rsplit(".", 1)[0] + ".bed"
fw = open(bedfile, "w")
for row in fp:
b = BlastLine(row)
if swap:
b = b.swapped
print >> fw, b.bedline
logging.debug("File written to `{0}`.".format(bedfile))
fw.close()
bed_sort([bedfile, "-i"])
return bedfile
def bed(args):
"""
%prog bed blastfile
Print out bed file based on coordinates in BLAST report. By default, write
out subject positions. Use --swap to write query positions.
"""
from jcvi.formats.bed import sort as bed_sort
p = OptionParser(bed.__doc__)
p.add_option("--swap", default=False, action="store_true",
help="Write query positions [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(p.print_help())
blastfile, = args
swap = opts.swap
fp = must_open(blastfile)
bedfile = blastfile.rsplit(".", 1)[0] + ".bed"
fw = open(bedfile, "w")
for row in fp:
b = BlastLine(row)
if swap:
b = b.swapped
print >> fw, b.bedline
logging.debug("File written to `{0}`.".format(bedfile))
fw.close()
bed_sort([bedfile, "-i"])
return bedfile
def bed(args):
"""
%prog bed blastfile
Print out bed file based on coordinates in BLAST report. By default, write
out subject positions. Use --swap to write query positions.
"""
from jcvi.formats.bed import sort as bed_sort
p = OptionParser(bed.__doc__)
p.add_option(
"--swap",
default=False,
action="store_true",
help="Write query positions",
)
p.add_option(
"--both",
default=False,
action="store_true",
help="Generate one line for each of query and subject",
)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(p.print_help())
(blastfile,) = args
positive = (not opts.swap) or opts.both
negative = opts.swap or opts.both
fp = must_open(blastfile)
bedfile = (
"{0}.bed".format(blastfile.rsplit(".", 1)[0])
if blastfile.endswith(".blast")
else "{0}.bed".format(blastfile)
)
fw = open(bedfile, "w")
for row in fp:
b = BlastLine(row)
if positive:
print(b.bedline, file=fw)
if negative:
print(b.swapped.bedline, file=fw)
logging.debug("File written to `%s`.", bedfile)
fw.close()
bed_sort([bedfile, "-i"])
return bedfile
def bed(args):
"""
%prog bed blastfile
Print out bed file based on coordinates in BLAST report. By default, write
out subject positions. Use --swap to write query positions.
"""
from jcvi.formats.bed import sort as bed_sort
p = OptionParser(bed.__doc__)
p.add_option("--swap", default=False, action="store_true",
help="Write query positions [default: %default]")
p.add_option("--both", default=False, action="store_true",
help="Generate one line for each of query and subject")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(p.print_help())
blastfile, = args
positive = (not opts.swap) or opts.both
negative = opts.swap or opts.both
fp = must_open(blastfile)
bedfile = "{0}.bed".format(blastfile.rsplit(".", 1)[0]) \
if blastfile.endswith(".blast") \
else "{0}.bed".format(blastfile)
fw = open(bedfile, "w")
for row in fp:
b = BlastLine(row)
if positive:
print(b.bedline, file=fw)
if negative:
print(b.swapped.bedline, file=fw)
logging.debug("File written to `{0}`.".format(bedfile))
fw.close()
bed_sort([bedfile, "-i"])
return bedfile
