-
Notifications
You must be signed in to change notification settings - Fork 2
/
mergeUnmapped.py
executable file
·55 lines (53 loc) · 2.26 KB
/
mergeUnmapped.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# mergeUnmapped.py
#
# Copyright 2017 Huan Fan
# <hfan22@wisc.edu> & Yann Surget-Groba <yann@xtbg.org.cn>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
import sys,gzip,os
def smartopen(filename, mode = 'rt'):
import gzip, bz2
if filename.endswith('gz'):
return gzip.open(filename, mode)
elif filename.endswith('bz2'):
return bz2.BZ2File(filename, mode)
else:
return open(filename,*args,**kwargs)
if __name__ == '__main__':
dataDir = sys.argv[1].rstrip('/')
swapdic = {}
out_sh = open(dataDir + '_merge.sh','w')
for fileName in os.listdir(dataDir):
if not os.path.isdir(os.path.join(dataDir, fileName)):
if not fileName.startswith('.'):
if 'R1' in fileName:
with smartopen(dataDir + '/' + fileName) as fh:
tag = fh.readline()
if tag.startswith('@SRR'):
swapdic[fileName.split('_')[0]] = tag.split('.')[0].lstrip('@')
else:
swapdic[fileName.split('_')[0]] = tag.split(':')[0].lstrip('@')
for sample in swapdic:
command1 = 'zcat {}/{}_R1_unmapped.fq.gz | sed s/{}/{}/g | gzip >> {}/{}_unmapped1.fq.gz\n' \
.format(dataDir,sample,swapdic[sample],sample,dataDir,dataDir)
command2 = 'zcat {}/{}_R2_unmapped.fq.gz | sed s/{}/{}/g | gzip >> {}/{}_unmapped2.fq.gz\n' \
.format(dataDir,sample,swapdic[sample],sample,dataDir,dataDir)
out_sh.write(command1)
out_sh.write(command2)