makesitetrack.py

   1 #
   2 #  makesitetrack.py
   3 #  ENRAGE
   4 #
   5
   6 import sys, string, optparse
   7
   8 print "%prog: version 2.1"
   9
  10
  11 def main(argv=None):
  12     if not argv:
  13         argv = sys.argv
  14
  15     usage = "usage: python %prog sitefile outbedfile [--noheader] [--stype fieldID] [--color xx,yy,zz] [--append] [--exploded]"
  16
  17     parser = optparse.OptionParser(usage=usage)
  18     parser.add_option("--noheader", action="store_true", dest="noHeader")
  19     parser.add_option("--stype", type="int", dest="stypeID")
  20     parser.add_option("--color", dest="color")
  21     parser.add_option("--append", action="store_true", dest="append")
  22     parser.add_option("--exploded", action="store_false", dest="compact")
  23     parser.set_defaults(stypeID=None, color="0,0,0", append=False, compact=True, noHeader=False)
  24     (options, args) = parser.parse_args(argv[1:])
  25
  26     if len(args) < 2:
  27         print usage
  28         sys.exit(1)
  29
  30     infile = args[0]
  31     outfileName = args[1]
  32
  33     makesitetrack(infile, outfileName, options.stypeID, options.color, options.append, options.compact, options.noHeader)
  34
  35
  36 def makesitetrack(infileName, outFileName, stypeID=None, color="0,0,0", append=False, compact=True, noHeader=False):
  37     if stypeID is not None:
  38         doStype = True
  39     else:
  40         doStype = False
  41         stypeID = 4
  42
  43     infile = open(infileName)
  44
  45     if append:
  46         outfile = open(outFileName, "a")
  47     else:
  48         outfile = open(outFileName, "w")
  49
  50     try:
  51         (name, extension) = outFileName.split(".")
  52     except ValueError:
  53         name = outFileName.split(".")[:-1]
  54         name = string.join(name, "_")
  55
  56     if not noHeader:
  57         outfile.write('track name="%s" visibility=4 itemRgb="On"\n' % name)
  58
  59     count = 1
  60     for line in infile:
  61         if line[0] == "#":
  62             continue
  63
  64         fields = line.split()
  65         if compact:
  66             (chrom, loc) = fields[0].split(":")
  67             (start, stop) = loc.split("-")
  68             score = fields[1]
  69         else:
  70             chrom = fields[1]
  71             start = fields[2]
  72             stop = fields[3]
  73             score = 1.
  74
  75         stype = "%s-%s" % (name, str(count))
  76         if doStype:
  77             try:
  78                 stype = fields[stypeID]
  79                 if stype == "11":
  80                     stype = "can"
  81                 elif stype == "0":
  82                     stype = "half"
  83                 else:
  84                     stype = "NC" + stype
  85             except IndexError:
  86                 pass
  87
  88         sense = fields[-2].strip()
  89         if sense not in ["+", "-"]:
  90             sense = "+"
  91
  92         outfile.write("%s\t%s\t%d\t%s\t%s\t%s\t-\t-\t%s\n" % (chrom, start, int(stop) + 1, stype, score, sense, color))
  93         count += 1
  94
  95     outfile.close()
  96
  97
  98 if __name__ == "__main__":
  99     main(sys.argv)