chiapet/segregateLinkers.py

   1 import sys
   2
   3
   4 def main(argv=None):
   5     if not argv:
   6         argv = sys.argv
   7
   8     infile1 = argv[1]
   9     infile2 = argv[2]
  10     outprefix = argv[3]
  11
  12     segregateLinkers(infile1, infile2, outprefix)
  13
  14
  15 def segregateLinkers(infile1name, infile2name, outprefix):
  16     infile1 = open(infile1name)
  17     infile2 = open(infile2name)
  18     same1 = 0
  19     same2 = 0
  20     mixed = 0
  21     hasNA = 0
  22
  23     outsame1 = open("%s.same1.fa" % outprefix, "w")
  24     outsame2 = open("%s.same2.fa" % outprefix, "w")
  25     outNA = open("%s.NA.fa" % outprefix, "w")
  26     outmixed = open("%s.mixed.fa" % outprefix, "w")
  27
  28     lines1 = infile1.readlines()
  29
  30     failed = False
  31     for line1 in lines1:
  32         line2 = infile2.readline()
  33         if failed:
  34             line2 = infile2.readline()
  35             print line1.strip()
  36             print line2.strip()
  37             sys.exit(1)
  38             continue
  39
  40         if ">" in line1:
  41             try:
  42                 (linker1, readid1) = line1.split("_")
  43                 (linker2, readid2) = line2.split("_")
  44                 shortid1 = readid1.split("/")[0]
  45                 shortid2 = readid2.split("/")[0]
  46                 if shortid1 != shortid2:
  47                     print shortid1, shortid2
  48                     sys.exit(1)
  49
  50                 failed = False
  51             except:
  52                 print line1.strip()
  53                 print line2.strip()
  54                 failed = True
  55
  56             continue
  57
  58         if "NA" in linker1 or "NA" in linker2:
  59             hasNA += 1
  60             outNA.write("%s_%s%s" % (linker1, readid1, line1))
  61             outNA.write("%s_%s%s" % (linker2, readid2, line2))
  62         elif linker1 == linker2:
  63             if "L1" in linker1:
  64                 same1 += 1
  65                 outsame1.write("%s_%s%s" % (linker1, readid1, line1))
  66                 outsame1.write("%s_%s%s" % (linker2, readid2, line2))
  67             else:
  68                 same2 += 1
  69                 outsame2.write("%s_%s%s" % (linker1, readid1, line1))
  70                 outsame2.write("%s_%s%s" % (linker2, readid2, line2))
  71         else:
  72             mixed += 1
  73             outmixed.write("%s_%s%s" % (linker1, readid1, line1))
  74             outmixed.write("%s_%s%s" % (linker2, readid2, line2))
  75
  76     print same1
  77     print same2
  78     print mixed
  79     print hasNA
  80
  81     outmixed.close()
  82     outNA.close()
  83     outsame1.close()
  84     outsame2.close()
  85
  86
  87 if __name__ == "__main__":
  88     main(sys.argv)