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#!/usr/bin/python
import sys
import argparse
from pbsuite.utils import VCFIO
USAGE = "Turn .spots results into a .bed"
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=USAGE, \
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("input", metavar="SPOTS", default='-', nargs="?", \
help="Results to convert (stdin)")
parser.add_argument("-b", "--brief", action="store_true",\
help="Only output columns 1-4 of .bed")
args = parser.parse_args()
if args.input == '-':
fh = sys.stdin
else:
fh = open(args.input,'r')
for line in fh.readlines():
if line.startswith("##"):
continue
elif line.startswith("#"):
h = line.strip()[1:]
header = {}
for pos, item in enumerate(h.split('\t')):
header[item] = pos
continue
chrom, s, e, type, size, info = line.strip().split('\t')
name = "%s.%s" % (type, size)
print "\t".join([chrom, s, e, name, type, size])
fh.close()
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