regiontobed.py

   1 """
   2     usage: python regiontobed label regionfile outbedfile [--color r,g,b] [--score field] [--narrowPeak] [--broadPeak] [--itemRgb] [--nolabel]
   3            where color is in comma-delimited RGB without space
   4            and field is a column with a score (first column is 0, second is 1,...)
   5            t-narrowPeak assumes that findall.py was run with -listPeak
   6            t-broadPeak assumes that findall.py was *NOT* run with -listPeak
   7 """
   8
   9 try:
  10     import psyco
  11     psyco.full()
  12 except:
  13     pass
  14
  15 import sys, math, optparse
  16
  17 print "%prog: version 3.1"
  18
  19
  20 def usage():
  21     print __doc__
  22
  23
  24 def main(argv=None):
  25     if not argv:
  26         argv = sys.argv
  27
  28     usage = __doc__
  29
  30     parser = optparse.OptionParser(usage=usage)
  31     parser.add_option("--color", dest="color")
  32     parser.add_option("--score", type="int", dest="scoreField")
  33     parser.add_option("--narrowPeak", action="store_true", dest="doNarrow")
  34     parser.add_option("--broadPeak", action="store_true", dest="doBroad")
  35     parser.add_option("--itemRgb", action="store_true", dest="itemRGB")
  36     parser.add_option("--nolabel", action="store_true", dest="noLabel")
  37     parser.set_defaults(color="0,0,0", scoreField=None, doNarrow=False,
  38                         doBroad=False, itemRGB=False, noLabel=False)
  39     (options, args) = parser.parse_args(argv[1:])
  40
  41     if len(args) < 3:
  42         usage()
  43         sys.exit(2)
  44
  45     factorlabel = args[0]
  46     regionfile = args[1]
  47     outfile = args[2]
  48
  49     regiontobed(factorlabel, regionfile, outfile, options.color,
  50                 options.scoreField, options.doNarrow, options.doBroad,
  51                 options.itemRGB, options.noLabel)
  52
  53
  54 def regiontobed(factorlabel, regionFileName, outFileName, color="0,0,0",
  55                 scoreField=None, doNarrow=False, doBroad=False, itemRGB=False,
  56                 noLabel=False):
  57
  58     regionfile = open(regionFileName)
  59     outfile = open(outFileName, "w")
  60
  61     if itemRGB:
  62         print "assigning each item its color"
  63
  64     if noLabel:
  65         if itemRGB:
  66             outfile.write('track name=%s visibility=4 itemRgb="on"\n' % factorlabel)
  67         else:
  68             outfile.write("track name=%s visibility=4 color=%s\n" % (factorlabel, color))
  69
  70     for line in regionfile:
  71         if line[0] == "#":
  72             continue
  73
  74         fields = line.strip().split()
  75         if doNarrow:
  76             signalVal = float(fields[4])
  77             pval = float(fields[-1])
  78             if pval == 0.:
  79                 pValue = 350
  80             else:
  81                 pValue = -1. * math.log(pval, 10)
  82
  83             peakPos = int(fields[9]) - int(fields[2])
  84             outfile.write("%s\t%s\t%s\t%s\t%d\t.\t%.4f\t%.4f\t-1\t%d" % (fields[1], fields[2], fields[3], fields[0], 0, signalVal, pValue, peakPos))
  85         elif doBroad:
  86             signalVal = float(fields[4])
  87             pval = float(fields[-1])
  88             if pval == 0.:
  89                 pValue = 350
  90             else:
  91                 pValue = -1. * math.log(pval, 10)
  92
  93             outfile.write("%s\t%s\t%s\t%s\t%d\t.\t%.4f\t%.4f\t-1" % (fields[1], fields[2], fields[3], fields[0], 0, signalVal, pValue))
  94         elif scoreField is not None:
  95             score = int(float(fields[scoreField]))
  96             if score > 1000:
  97                 score = 1000
  98
  99             outfile.write("%s\t%s\t%s\t%s\t%s" % (fields[1], fields[2], fields[3], fields[0], score))
 100             if itemRGB:
 101                 outfile.write("\t+\t-\t-\t%s" % color)
 102         else:
 103             outfile.write("%s\t%s\t%s\t%s" % (fields[1], fields[2], fields[3], fields[0]))
 104             if itemRGB:
 105                 outfile.write("\t1000\t+\t-\t-\t%s" % color)
 106
 107         outfile.write("\n")
 108
 109     outfile.close()
 110
 111
 112 if __name__ == "__main__":
 113     main(sys.argv)