Mercurial > repos > bgruening > bismark

annotate bismark2report_wrapper.py @ 16:a4504327c890 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
author bgruening
date Wed, 21 Aug 2019 12:59:48 -0400
parents 9bfe38410155
children 120b7b35e442
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
1 #!/usr/bin/python
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
2
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
3 import argparse
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
4 import logging
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
5 import subprocess
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
6 import sys
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
7
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
8
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
9 def stop_err(logger, msg):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
10 logger.critical(msg)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
11 sys.exit()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
12
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
13
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
14 def log_subprocess_output(logger, pipe):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
15 for line in iter(pipe.readline, b''):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
16 logger.debug(line.decode().rstrip())
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
17
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
18
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
19 def get_arg():
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
20 parser = argparse.ArgumentParser()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
21 parser.add_argument('--alignment_report', dest='alignment_report', action='store', metavar='alignment_report',
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
22 type=str)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
23 parser.add_argument('--dedup_report', dest='dedup_report', action='store', metavar='dedup_report', type=str)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
24 parser.add_argument('--splitting_report', dest='splitting_report', action='store', metavar='splitting_report',
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
25 type=str)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
26 parser.add_argument('--mbias_report', dest='mbias_report', action='store', metavar='mbias_report', type=str)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
27 parser.add_argument('--nucleotide_report', dest='nucleotide_report', action='store', metavar='nucleotide_report',
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
28 type=str)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
29 parser.add_argument('--output_html_report', dest='output_html_report', action='store', metavar='output_html_report',
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
30 type=str)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
31 parser.add_argument('--log_report', dest='log_report', action='store', metavar='log_report', type=str)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
32 args = parser.parse_args()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
33 return args
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
34
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
35
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
36 def __main__():
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
37 args = get_arg()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
38 logger = logging.getLogger('bismark_deduplicate_wrapper')
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
39 logger.setLevel(logging.DEBUG)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
40 ch = logging.StreamHandler(sys.stdout)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
41 if args.log_report:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
42 ch.setLevel(logging.WARNING)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
43 handler = logging.FileHandler(args.log_report)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
44 handler.setLevel(logging.DEBUG)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
45 logger.addHandler(handler)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
46 else:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
47 ch.setLevel(logging.DEBUG)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
48 logger.addHandler(ch)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
49
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
50 cmd = ['bismark2report', '--verbose', '--alignment_report', args.alignment_report,
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
51 '--output', args.output_html_report]
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
52
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
53 if args.dedup_report:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
54 cmd.extend(['--dedup_report', args.dedup_report])
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
55 if args.splitting_report:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
56 cmd.extend(['--splitting_report', args.splitting_report])
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
57 if args.mbias_report:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
58 cmd.extend(['--mbias_report', args.mbias_report])
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
59 if args.nucleotide_report:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
60 cmd.extend(['--nucleotide_report', args.nucleotide_report])
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
61
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
62 logger.info("Generating report with: '%s'", " ".join(cmd))
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
63 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
64 with process.stdout:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
65 log_subprocess_output(logger, process.stdout)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
66 exitcode = process.wait()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
67 if exitcode != 0:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
68 stop_err(logger, "Bismark pretty report error (also check the log file if any)!\n%s" % process.stderr)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
69
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
70
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
71 if __name__ == "__main__": __main__()