bedtoregion.py

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