Mercurial > repos > crs4 > mugsy

comparison mugsy.py @ 2:13f806b78483 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add Boost requirement.
author crs4
date Fri, 25 Oct 2013 06:39:33 -0400
parents 1e8862eb2eba
children
comparison
equal deleted inserted replaced
1:2dcf5873f1b1 2:13f806b78483
11 import subprocess 11 import subprocess
12 import sys 12 import sys
13 import tempfile 13 import tempfile
14 14
15 def __main__(): 15 def __main__():
16 """ main function """
17 parser = optparse.OptionParser() 16 parser = optparse.OptionParser()
18 parser.add_option('-r', dest='reference', help='reference FASTA file') 17 parser.add_option('-r', dest='reference', help='reference FASTA file')
19 parser.add_option('-c', dest='contigs', help='contigs FASTA file') 18 parser.add_option('-c', dest='contigs', help='contigs FASTA file')
20 parser.add_option('-p', dest='prefix', default='prefix', help='prefix ') 19 parser.add_option('-p', dest='prefix', default='prefix', help='prefix ')
21 parser.add_option('-l', dest='logfile', help='logfile') 20 parser.add_option('-l', dest='logfile', help='logfile')
22 parser.add_option('--ml', dest='mugsylog', help='mugsylog file') 21 parser.add_option('--ml', dest='mugsylog', help='mugsylog file')
23 parser.add_option('--maf', dest='maf', help='ouput MAF alignment file ') 22 parser.add_option('--maf', dest='maf', help='ouput MAF alignment file ')
24 (options, args) = parser.parse_args() 23 (options, args) = parser.parse_args()
25 if len(args) > 0: 24 if len(args) > 0:
26 parser.error('Wrong number of arguments') 25 parser.error('Wrong number of arguments')
27 26
28 logfile = options.logfile 27 logfile = options.logfile
29 wd = tempfile.mkdtemp() 28 wd = tempfile.mkdtemp()
30 try: 29 try:
31 command = "mugsy --directory %s --prefix %s --log %s %s %s" % (wd, options.prefix, options.mugsylog, options.reference, options.contigs) 30 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 31 print 'Mugsy command to be executed:\n ' + command
33 32
34 log = open(logfile, 'w') if logfile else sys.stdout 33 log = open(logfile, 'w') if logfile else sys.stdout
35 try: 34 try:
36 subprocess.check_call(command, stderr=log, shell=True) # need to redirect stderr because mugsy writes its logging info there 35 subprocess.check_call(command, stderr=log, shell=True) # need to redirect stderr because mugsy writes its logging info there
37 finally: 36 finally:
38 if log != sys.stdout: 37 if log != sys.stdout:
39 log.close() 38 log.close()
40 print 'Mugsy executed!' 39 print 'Mugsy executed!'
41 40
42 shutil.move(os.path.join(wd, options.prefix + '.maf'), options.maf) 41 shutil.move(os.path.join(wd, options.prefix + '.maf'), options.maf)
43 finally: 42 finally:
44 shutil.rmtree(wd) 43 shutil.rmtree(wd)
45 44
46 45