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#!/usr/bin/python3 -O
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
#Generating insert size distribution from raw file
import sys
if len(sys.argv) < 5:
print("Usage: <input raw file> <output> <min is> <max is> [fr/rf], fr -- default, rf -- calculate insert size for rf pairs as for chimeric")
exit(0)
inFile = open(sys.argv[1])
outFile = open(sys.argv[2], 'w')
minLen = int(sys.argv[3])
maxLen = int(sys.argv[4])
fr = True
if len(sys.argv) > 5 and sys.argv[5] == "rf":
rf = False
hist = [0 for i in range(maxLen + 1)]
while (1):
line = inFile.readline()
if not line:
break
pos1 = int(line.split(' ')[0])
len1 = int(line.split(' ')[1])
line = inFile.readline()
if not line:
break
pos2 = int(line.split(' ')[0])
len2 = int(line.split(' ')[1])
if fr:
cord = pos2 - pos1 + len2
else:
cord = pos1 + len1 - pos2
if cord < maxLen and cord > minLen:
hist[cord] += 1
sum = 0
for i in range(minLen,maxLen):
sum += hist[i]
outFile.write(str(i) + ' ' + str(hist[i]) + '\n')
print("Total mate-pairs: " + str(sum))
inFile.close()
outFile.close()
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