Mercurial > repos > devteam > sam2interval

annotate sam2interval.py @ 1:75557c0908a9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
author devteam
date Wed, 05 Feb 2020 06:58:53 -0500
parents 8c737b8ddc45
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
1 #!/usr/bin/env python
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
2
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
3 import sys
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
4 import optparse
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
5 import re
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
6
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
7
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
8 def stop_err(msg):
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
9 sys.exit(msg)
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
10
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
11
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
12 def main():
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
13 usage = """%prog [options]
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
14
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
15 options (listed below) default to 'None' if omitted
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
16 """
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
17 parser = optparse.OptionParser(usage=usage)
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
18
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
19 parser.add_option(
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
20 '-f', '--input_sam_file',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
21 metavar="INPUT_SAM_FILE",
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
22 dest='input_sam',
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
23 default=False,
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
24 help='Name of the SAM file to be filtered. STDIN is default')
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
25
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
26 parser.add_option(
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
27 '-c', '--flag_column',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
28 dest='flag_col',
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
29 default='2',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
30 help='Column containing SAM bitwise flag. 1-based')
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
31
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
32 parser.add_option(
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
33 '-s', '--start_column',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
34 dest='start_col',
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
35 default='4',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
36 help='Column containing position. 1-based')
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
37
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
38 parser.add_option(
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
39 '-g', '--cigar_column',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
40 dest='cigar_col',
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
41 default='6',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
42 help='Column containing CIGAR or extended CIGAR string')
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
43
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
44 parser.add_option(
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
45 '-r', '--ref_column',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
46 dest='ref_col',
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
47 default='3',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
48 help='Column containing name of the reference sequence coordinate. 1-based')
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
49
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
50 parser.add_option(
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
51 '-e', '--read_column',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
52 dest='read_col',
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
53 default='1',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
54 help='Column containing read name. 1-based')
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
55
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
56 parser.add_option(
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
57 '-p', '--print_all',
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
58 dest='prt_all',
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
59 action='store_true',
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
60 default=False,
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
61 help='Print coordinates and original SAM?')
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
62
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
63 options, args = parser.parse_args()
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
64
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
65 if options.input_sam:
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
66 infile = open(options.input_sam, 'r')
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
67 else:
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
68 infile = sys.stdin
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
69
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
70 cigar = re.compile('\d+M|\d+N|\d+D|\d+P')
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
71
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
72 print('#chrom\tstart\tend\tstrand\tread_name') # provide a (partial) header so that strand is automatically set in metadata
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
73
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
74 for line in infile:
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
75 line = line.rstrip('\r\n')
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
76 if line and not line.startswith('#') and not line.startswith('@'):
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
77 fields = line.split('\t')
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
78 start = int(fields[int(options.start_col) - 1]) - 1
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
79 end = 0
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
80 for op in cigar.findall(fields[int(options.cigar_col) - 1]):
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
81 end += int(op[0:len(op) - 1])
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
82
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
83 strand = '+'
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
84 if bool(int(fields[int(options.flag_col) - 1]) & 0x0010):
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
85 strand = '-'
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
86 read_name = fields[int(options.read_col) - 1]
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
87 ref_name = fields[int(options.ref_col) - 1]
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
88
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
89 if ref_name != '*':
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
90 # Do not print lines with unmapped reads that contain '*' instead of chromosome name
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
91 if options.prt_all:
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
92 print('%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end + start), strand, line))
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
93 else:
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
94 print('%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end + start), strand, read_name))
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
95
0
8c737b8ddc45 Uploaded tool tarball.
devteam
parents:
diff changeset
96
1
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
97 if __name__ == "__main__":
75557c0908a9 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval commit 206cd8245e7619b0e924c5066d0172129222993d"
devteam
parents: 0
diff changeset
98 main()