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#!/usr/bin/python3
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
#Merge two single-read bowtie logs into paired one
import sys
import os
if len(sys.argv) != 3:
print("Usage: " + sys.argv[0] + " <1st bowtie log> <2nd bowtie log>")
sys.exit()
rFileName1 = sys.argv[1]
rFileName2 = sys.argv[2]
rFile1 = open(rFileName1, "r")
rFile2 = open(rFileName2, "r")
pc = 0
c1 = 0
c2 = 0
ids = {}
for line in rFile1:
id1 = line.split('/', 1)[0]
ids[id1] = line
c1 += 1
fName1, ext1 = os.path.splitext(rFileName1)
outFile = open(fName1 + "_paired" + ext1, "w")
for line in rFile2:
c2 += 1
id2 = line.split('/', 1)[0]
if id2 in ids:
pc += 1
outFile.write(ids[id2] + line)
print("1: " + str(c1) + " 2: " + str(c2) + " Pairs: " + str(pc) + "\n")
rFile1.close()
rFile2.close()
outFile.close()
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