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 "%s: version 1.0" % sys.argv[0]
  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     radius = 500
  28     chromField = 2
  29     posField = 3
  30     labelField = 1
  31     dataField = -1
  32
  33     if len(argv) > 3:
  34         radius = int(argv[3])
  35
  36     if len(argv) > 4:
  37         chromField = int(argv[4])
  38
  39     if len(argv) > 5:
  40         posField = int(argv[5])
  41
  42     if len(argv) > 6:
  43         labelField = int(argv[6])
  44
  45     if len(argv) > 7:
  46         dataField = int(argv[7])
  47
  48     peakstoregion(peakfile, outfile, radius, chromField, posField, labelField, dataField)
  49
  50
  51 def peakstoregion(peakfilename, outfilename, radius=500, chromField=2, posField=3, labelField=1, dataField=-1):
  52     peakfile = open(peakfilename)
  53     outfile = open(outfilename, "w")
  54
  55     for line in peakfile:
  56         fields = line.strip().split()
  57         label = "REGION"
  58         try:
  59             label = fields[labelField]
  60         except IndexError:
  61             pass
  62
  63         start = int(fields[posField]) - radius
  64         stop = int(fields[posField]) + radius
  65         outfile.write("%s\t%s\t%d\t%d\t%s\n" % (label, fields[chromField], start, stop, fields[dataField]))
  66
  67     outfile.close()
  68
  69
  70 if __name__ == "__main__":
  71     main(sys.argv)