rnaAToIFilter.py

   1 import sys
   2
   3
   4 def main(argv=None):
   5     if not argv:
   6         argv = sys.argv
   7
   8     usage = "usage: python %s infile outfile" % sys.argv[0]
   9
  10     if len(argv) < 3:
  11         print usage
  12         sys.exit(1)
  13
  14     infile = open(argv[1])
  15     outfile = open(argv[2], "w")
  16
  17     lines = infile.readlines()
  18     outputLines = rnaAToIFilter(lines)
  19
  20     for line in outputLines:
  21         outfile.write(line)
  22
  23     outfile.close()
  24
  25
  26 def rnaAToIFilter(snpPropertiesList):
  27     outputLines = []
  28     for line in snpPropertiesList:
  29         fields = line.split()
  30         if fields[13] == "F" and fields[7] == "A-G":
  31             outputLines.append(line)
  32         elif fields[13] == "R" and fields[7] == "T-C":
  33             outputLines.append(line)
  34
  35     return outputLines
  36
  37
  38 if __name__ == '__main__':
  39     pass