Mercurial > repos > crs4 > mugsy
comparison mugsy.py @ 0:1e8862eb2eba draft
Uploaded
| author | crs4 |
|---|---|
| date | Fri, 06 Sep 2013 05:58:59 -0400 |
| parents | |
| children | 13f806b78483 |
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| -1:000000000000 | 0:1e8862eb2eba |
|---|---|
| 1 # -*- coding: utf-8 -*- | |
| 2 """ | |
| 3 Mugsy wrapper | |
| 4 | |
| 5 For draft genomes a single multi-FASTA file containig all contigs should be provided. | |
| 6 """ | |
| 7 | |
| 8 import optparse | |
| 9 import os | |
| 10 import shutil | |
| 11 import subprocess | |
| 12 import sys | |
| 13 import tempfile | |
| 14 | |
| 15 def __main__(): | |
| 16 """ main function """ | |
| 17 parser = optparse.OptionParser() | |
| 18 parser.add_option('-r', dest='reference', help='reference FASTA file') | |
| 19 parser.add_option('-c', dest='contigs', help='contigs FASTA file') | |
| 20 parser.add_option('-p', dest='prefix', default='prefix', help='prefix ') | |
| 21 parser.add_option('-l', dest='logfile', help='logfile') | |
| 22 parser.add_option('--ml', dest='mugsylog', help='mugsylog file') | |
| 23 parser.add_option('--maf', dest='maf', help='ouput MAF alignment file ') | |
| 24 (options, args) = parser.parse_args() | |
| 25 if len(args) > 0: | |
| 26 parser.error('Wrong number of arguments') | |
| 27 | |
| 28 logfile = options.logfile | |
| 29 wd = tempfile.mkdtemp() | |
| 30 try: | |
| 31 command = "mugsy --directory %s --prefix %s --log %s %s %s" % (wd, options.prefix, options.mugsylog, options.reference, options.contigs) | |
| 32 print 'Mugsy command to be executed:\n ' + command | |
| 33 | |
| 34 log = open(logfile, 'w') if logfile else sys.stdout | |
| 35 try: | |
| 36 subprocess.check_call(command, stderr=log, shell=True) # need to redirect stderr because mugsy writes its logging info there | |
| 37 finally: | |
| 38 if log != sys.stdout: | |
| 39 log.close() | |
| 40 print 'Mugsy executed!' | |
| 41 | |
| 42 shutil.move(os.path.join(wd, options.prefix + '.maf'), options.maf) | |
| 43 finally: | |
| 44 shutil.rmtree(wd) | |
| 45 | |
| 46 | |
| 47 if __name__ == "__main__": | |
| 48 __main__() |