Mercurial > repos > genouest > get_pairs
comparison get_pairs.py @ 0:ac738de70427 draft default tip
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
author | genouest |
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date | Mon, 10 Sep 2018 10:16:42 -0400 (2018-09-10) |
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-1:000000000000 | 0:ac738de70427 |
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1 #!/opt/python/bin/python | |
2 # -*- coding: utf-8 -*- | |
3 # ---------------------------------------------------------- | |
4 # -- | |
5 # -- author : Pierre Pericard | |
6 # -- created : 2012-11-09 | |
7 # -- modified: 2013-05-23 | |
8 # -- | |
9 # ---------------------------------------------------------- | |
10 # -- | |
11 # -- description : Get separately paired reads and singletons | |
12 # -- from two fastq files (left and right) | |
13 # -- | |
14 # -- get_pairs.py file1.fastq file2.fastq | |
15 # -- | |
16 # ---------------------------------------------------------- | |
17 | |
18 import argparse | |
19 import sys | |
20 | |
21 | |
22 if __name__ == '__main__': | |
23 | |
24 # Arguments | |
25 parser = argparse.ArgumentParser(description='Get separately paired reads and singletons from two fastq files (left and right)') | |
26 parser.add_argument('leftreads', metavar='leftreads', type=argparse.FileType('r'), help='left reads fastq') | |
27 parser.add_argument('rightreads', metavar='rightreads', type=argparse.FileType('r'), help='right reads fastq') | |
28 | |
29 args = parser.parse_args() | |
30 | |
31 leftreads = args.leftreads.name | |
32 rightreads = args.rightreads.name | |
33 | |
34 (n1, n2) = (list(), list()) | |
35 | |
36 for f, n in ((leftreads, n1), (rightreads, n2)): | |
37 with open(f, 'r') as fh: | |
38 c = 0 | |
39 for line in fh: | |
40 line = line.strip() | |
41 if line: | |
42 c += 1 | |
43 if c % 4 == 1: | |
44 n.append(line.split()[0][1:].split('/')[0]) | |
45 if c % 40000 == 1: | |
46 sys.stdout.write("\r%.2f M reads read" % (c / 4000000.0)) | |
47 sys.stdout.write("\r%.2f M reads read\n" % (c / 4000000.0)) | |
48 | |
49 notcommon = set(n1) ^ set(n2) | |
50 | |
51 for f in (leftreads, rightreads): | |
52 | |
53 if f == leftreads: | |
54 basefilename = "left" | |
55 else: | |
56 basefilename = "right" | |
57 | |
58 pfh = open(basefilename + '.paired.fastq', 'w') | |
59 ufh = open(basefilename + '.unpaired.fastq', 'w') | |
60 with open(f, 'r') as fh: | |
61 c = 0 | |
62 paired = False | |
63 for line in fh: | |
64 line = line.strip() | |
65 if line: | |
66 c += 1 | |
67 if c % 4 == 1: | |
68 paired = line.split()[0][1:].split('/')[0] not in notcommon | |
69 if c % 40000 == 1: | |
70 sys.stdout.write("\r%.2f M reads writen" % (c / 4000000.0)) | |
71 if paired: | |
72 pfh.write("%s\n" % line) | |
73 else: | |
74 ufh.write("%s\n" % line) | |
75 sys.stdout.write("\r%.2f M reads writen\n" % (c / 4000000.0)) | |
76 pfh.close() | |
77 ufh.close() |