bedtoregion.py

   1 import sys
   2 import string
   3
   4 def main(argv=None):
   5     if not argv:
   6         argv = sys.argv
   7
   8     usage = "usage: python %s factorlabel bedinfilename regionoutfile" % sys.argv[0]
   9
  10     if len(argv) < 4:
  11         print usage
  12         sys.exit(1)
  13
  14     factor = argv[1]
  15     infilename = argv[2]
  16     outfilename = argv[3]
  17
  18     bedToRegion(factor, infilename, outfilename)
  19
  20
  21 def bedToRegion(factor, infilename, outfilename):
  22     index = 1
  23     infile = open(infilename)
  24     outfile = open(outfilename, "w")
  25     for line in infile:
  26         if "track" in line:
  27             continue
  28
  29         fields = line.split()
  30         line = string.join(fields, "\t")
  31         outfile.write("%s%d\t%s\n" % (factor, index, line))
  32         index += 1
  33
  34     infile.close()
  35     outfile.close()
  36
  37 if __name__ == "__main__":
  38     main(sys.argv)