12 segregateLinkers(infile1, infile2, outprefix)
15 def segregateLinkers(infile1name, infile2name, outprefix):
16 infile1 = open(infile1name)
17 infile2 = open(infile2name)
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")
28 lines1 = infile1.readlines()
32 line2 = infile2.readline()
34 line2 = infile2.readline()
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
58 if "NA" in linker1 or "NA" in linker2:
60 outNA.write("%s_%s%s" % (linker1, readid1, line1))
61 outNA.write("%s_%s%s" % (linker2, readid2, line2))
62 elif linker1 == linker2:
65 outsame1.write("%s_%s%s" % (linker1, readid1, line1))
66 outsame1.write("%s_%s%s" % (linker2, readid2, line2))
69 outsame2.write("%s_%s%s" % (linker1, readid1, line1))
70 outsame2.write("%s_%s%s" % (linker2, readid2, line2))
73 outmixed.write("%s_%s%s" % (linker1, readid1, line1))
74 outmixed.write("%s_%s%s" % (linker2, readid2, line2))
87 if __name__ == "__main__":