Mercurial > repos > konradpaszkiewicz > velvetoptimiser
comparison velvet_optimiser.py @ 0:50ae1360fbbe default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | konradpaszkiewicz |
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date | Tue, 07 Jun 2011 18:07:56 -0400 |
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-1:000000000000 | 0:50ae1360fbbe |
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1 #!/usr/bin/env python | |
2 | |
3 """ | |
4 VelvetOptimiser Wrapper | |
5 Adapted from velveth and velvetg tools in Galaxy | |
6 Konrad Paszkiewicz University of Exeter, UK. | |
7 | |
8 """ | |
9 import pkg_resources; | |
10 import logging, os, string, sys, tempfile, glob, shutil, types, urllib | |
11 import shlex, subprocess | |
12 from optparse import OptionParser, OptionGroup | |
13 from stat import * | |
14 | |
15 | |
16 log = logging.getLogger( __name__ ) | |
17 | |
18 assert sys.version_info[:2] >= ( 2, 4 ) | |
19 | |
20 def stop_err( msg ): | |
21 sys.stderr.write( "%s\n" % msg ) | |
22 sys.exit() | |
23 | |
24 def __main__(): | |
25 #Parse Command Line | |
26 s = 'velvetg_optimiser.py: argv = %s\n' % (sys.argv) | |
27 #print >> sys.stderr, s # so will appear as blurb for file | |
28 argcnt = len(sys.argv) | |
29 starthash = sys.argv[1] | |
30 endhash = sys.argv[2] | |
31 inputs = sys.argv[3] | |
32 threads = sys.argv[4] | |
33 afgFile = sys.argv[5] | |
34 kmeropt = sys.argv[6] | |
35 covopt = sys.argv[7] | |
36 contigs = sys.argv[8] | |
37 LastGraph = sys.argv[9] | |
38 velvet_asm = sys.argv[10] | |
39 unusedReadsFile = sys.argv[11] | |
40 stats = sys.argv[12] | |
41 othervelvetgoptions = sys.argv[13] | |
42 working_dir = '' | |
43 | |
44 cmdline = '/usr/local/velvet/contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl -s %s -e %s -f \' %s \' -t %s -a 1 -k %s -c %s -o \'-unused_reads yes %s\' 2&1>/dev/null' % (starthash, endhash, inputs, threads, kmeropt, covopt, othervelvetgoptions) | |
45 #print >> sys.stderr, cmdline # so will appear as blurb for file | |
46 try: | |
47 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) | |
48 returncode = proc.wait() | |
49 # get stderr, allowing for case where it's very large | |
50 stderr = '' | |
51 buffsize = 1048576 | |
52 try: | |
53 while True: | |
54 stderr += proc.stderr.read( buffsize ) | |
55 if not stderr or len( stderr ) % buffsize != 0: | |
56 break | |
57 except OverflowError: | |
58 pass | |
59 if returncode != 0: | |
60 raise Exception, stderr | |
61 except Exception, e: | |
62 stop_err( 'Error running velvet_optimiser.py' + str( e ) ) | |
63 | |
64 out = open(contigs,'w') | |
65 contigs_path = os.path.join(working_dir,'contigs.fa') | |
66 #print >> sys.stderr, contigs_path | |
67 for line in open(contigs_path ): | |
68 out.write( "%s" % (line) ) | |
69 out.close() | |
70 out = open(stats,'w') | |
71 stats_path = os.path.join(working_dir,'stats.txt') | |
72 for line in open( stats_path ): | |
73 out.write( "%s" % (line) ) | |
74 out.close() | |
75 if LastGraph != 'None': | |
76 out = open(LastGraph,'w') | |
77 LastGraph_path = os.path.join(working_dir,'LastGraph') | |
78 for line in open( LastGraph_path ): | |
79 out.write( "%s" % (line) ) | |
80 out.close() | |
81 if afgFile != 'None': | |
82 out = open(afgFile,'w') | |
83 afgFile_path = os.path.join(working_dir,'velvet_asm.afg') | |
84 try: | |
85 for line in open( afgFile_path ): | |
86 out.write( "%s" % (line) ) | |
87 except: | |
88 logging.warn( 'error reading %s' %(afgFile_path)) | |
89 pass | |
90 out.close() | |
91 if unusedReadsFile != 'None': | |
92 out = open(unusedReadsFile,'w') | |
93 unusedReadsFile_path = os.path.join(working_dir,'UnusedReads.fa') | |
94 try: | |
95 for line in open( unusedReadsFile_path ): | |
96 out.write( "%s" % (line) ) | |
97 except: | |
98 logging.info( 'error reading %s' %(unusedReadsFile_path)) | |
99 pass | |
100 out.close() | |
101 | |
102 if __name__ == "__main__": __main__() |