Mercurial > repos > peterjc > samtools_idxstats

annotate tools/samtools_idxstats/samtools_idxstats.py @ 2:71afa65f444a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.0.5 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 09:24:18 -0400
parents 8945bad80f4a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
1 #!/usr/bin/env python
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
2 """Wrapper for "samtools idxstats" for use in Galaxy.
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
3
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
4 This script takes exactly three command line arguments:
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
5 * Input BAM filename
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
6 * Input BAI filename (via Galaxy metadata)
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
7 * Output tabular filename
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
8
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
9 This messes about with the filenames to make samtools happy, then
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
10 runs "samtools idxstats" and captures the output to the desired
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
11 tabular file.
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
12 """
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
13
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
14 import os
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
15 import sys
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
16 import tempfile
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
17
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
18 if "-v" in sys.argv or "--version" in sys.argv:
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
19 # Galaxy seems to invert the order of the two lines
1
8945bad80f4a v0.0.4; internal changes for packaging
peterjc
parents: 0
diff changeset
20 print "(Galaxy wrapper v0.0.2)"
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
21 cmd = "samtools 2>&1 | grep -i ^Version"
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
22 sys.exit(os.system(cmd))
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
23
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
24 if len(sys.argv) != 4:
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
25 sys.exit("Require three arguments: BAM, BAI, tabular filenames")
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
26
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
27 bam_filename, bai_filename, tabular_filename = sys.argv[1:]
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
28
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
29 if not os.path.isfile(bam_filename):
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
30 sys.exit("Input BAM file not found: %s" % bam_filename)
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
31 if not os.path.isfile(bai_filename):
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
32 if bai_filename == "None":
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
33 sys.exit("Error: Galaxy did not index your BAM file")
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
34 sys.exit("Input BAI file not found: %s" % bai_filename)
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
35
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
36 # Assign sensible names with real extensions, and setup symlinks:
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
37 tmp_dir = tempfile.mkdtemp()
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
38 bam_file = os.path.join(tmp_dir, "temp.bam")
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
39 bai_file = os.path.join(tmp_dir, "temp.bam.bai")
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
40 os.symlink(os.path.abspath(bam_filename), bam_file)
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
41 os.symlink(os.path.abspath(bai_filename), bai_file)
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
42 assert os.path.isfile(bam_file), bam_file
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
43 assert os.path.isfile(bai_file), bai_file
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
44 assert os.path.isfile(bam_file + ".bai"), bam_file
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
45
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
46 # Run samtools idxstats:
1
8945bad80f4a v0.0.4; internal changes for packaging
peterjc
parents: 0
diff changeset
47 cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename)
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
48 return_code = os.system(cmd)
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
49
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
50 # Remove the temp symlinks:
0
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
51 os.remove(bam_file)
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
52 os.remove(bai_file)
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
53 os.rmdir(tmp_dir)
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
54
d4412c04d7b1 Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
peterjc
parents:
diff changeset
55 if return_code:
2
71afa65f444a v0.0.5 Internal changes to command line handling
peterjc
parents: 1
diff changeset
56 sys.exit("Return code %i from command:\n%s" % (return_code, cmd))