peakstoregion.py

   1 #
   2 #  peakstoregion.py
   3 #  ENRAGE
   4 #
   5
   6 try:
   7     import psyco
   8     psyco.full()
   9 except:
  10     pass
  11
  12 import sys
  13
  14 print "peakstoregion: version 1.1"
  15
  16 def main(argv=None):
  17     if not argv:
  18         argv = sys.argv
  19
  20     if len(argv) < 3:
  21         print "usage: python %s peakfile outfile [radius] [chromField] [posField] [labelField] [datafield]" % sys.argv[0]
  22         sys.exit(1)
  23
  24     peakfile = argv[1]
  25     outfile = argv[2]
  26
  27     try:
  28         radius = int(argv[3])
  29     except (IndexError, ValueError):
  30         radius = 500
  31
  32     try:
  33         chromField = int(argv[4])
  34     except (IndexError, ValueError):
  35         chromField = 2
  36
  37     try:
  38         posField = int(argv[5])
  39     except (IndexError, ValueError):
  40         posField = 3
  41
  42     try:
  43         labelField = int(argv[6])
  44     except (IndexError, ValueError):
  45         labelField = 1
  46
  47     try:
  48         dataField = int(argv[7])
  49     except (IndexError, ValueError):
  50         dataField = -1
  51
  52     peakstoregion(peakfile, outfile, radius, chromField, posField, labelField, dataField)
  53
  54
  55 def peakstoregion(peakfilename, outfilename, radius=500, chromField=2, posField=3, labelField=1, dataField=-1):
  56     peakfile = open(peakfilename)
  57     outfile = open(outfilename, "w")
  58
  59     for line in peakfile:
  60         fields = line.strip().split()
  61         label = "REGION"
  62         try:
  63             label = fields[labelField]
  64         except IndexError:
  65             pass
  66
  67         start = int(fields[posField]) - radius
  68         stop = int(fields[posField]) + radius
  69         outfile.write("%s\t%s\t%d\t%d\t%s\n" % (label, fields[chromField], start, stop, fields[dataField]))
  70
  71     outfile.close()
  72
  73
  74 if __name__ == "__main__":
  75     main(sys.argv)