def mergebed(args):
"""
%prog mergebed map1.bed map2.bed map3.bed ...
Combine bed maps to bed format, adding the map name.
"""
p = OptionParser(mergebed.__doc__)
p.add_option("-w",
"--weightsfile",
default="weights.txt",
help="Write weights to file")
p.set_outfile("out.bed")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
maps = args
outfile = opts.outfile
fp = must_open(maps)
b = Bed()
mapnames = set()
for row in fp:
mapname = fp.filename().split(".")[0]
mapnames.add(mapname)
try:
m = BedLine(row)
m.accn = "{0}-{1}".format(mapname, m.accn)
m.extra = ["{0}:{1}".format(m.seqid, m.start)]
b.append(m)
except (IndexError, ValueError): # header or mal-formed line
continue
b.print_to_file(filename=outfile, sorted=True)
logging.debug("A total of {0} markers written to `{1}`.".\
format(len(b), outfile))
assert len(maps) == len(mapnames), "You have a collision in map names"
write_weightsfile(mapnames, weightsfile=opts.weightsfile)
def mergebed(args):
"""
%prog mergebed map1.bed map2.bed map3.bed ...
Combine bed maps to bed format, adding the map name.
"""
p = OptionParser(mergebed.__doc__)
p.add_option("-w", "--weightsfile", default="weights.txt",
help="Write weights to file")
p.set_outfile("out.bed")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
maps = args
outfile = opts.outfile
fp = must_open(maps)
b = Bed()
mapnames = set()
for row in fp:
mapname = fp.filename().split(".")[0]
mapnames.add(mapname)
try:
m = BedLine(row)
m.accn = "{0}-{1}".format(mapname, m.accn)
m.extra = ["{0}:{1}".format(m.seqid, m.start)]
b.append(m)
except (IndexError, ValueError): # header or mal-formed line
continue
b.print_to_file(filename=outfile, sorted=True)
logging.debug("A total of {0} markers written to `{1}`.".\
format(len(b), outfile))
assert len(maps) == len(mapnames), "You have a collision in map names"
write_weightsfile(mapnames, weightsfile=opts.weightsfile)
