Mercurial > repos > xuebing > sharplabtool

comparison tools/sr_assembly/velvetg_wrapper.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2
3 """
4 Classes encapsulating decypher tool.
5 James E Johnson - University of Minnesota
6 """
7 import pkg_resources;
8 import logging, os, string, sys, tempfile, glob, shutil, types, urllib
9 import shlex, subprocess
10 from optparse import OptionParser, OptionGroup
11 from stat import *
12
13
14 log = logging.getLogger( __name__ )
15
16 assert sys.version_info[:2] >= ( 2, 4 )
17
18 def stop_err( msg ):
19 sys.stderr.write( "%s\n" % msg )
20 sys.exit()
21
22 def __main__():
23 #Parse Command Line
24 s = 'velvetg_wrapper.py: argv = %s\n' % (sys.argv)
25 # print >> sys.stderr, s # so will appear as blurb for file
26 argcnt = len(sys.argv)
27 working_dir = sys.argv[1]
28 contigs = sys.argv[2]
29 stats = sys.argv[3]
30 LastGraph = sys.argv[4]
31 afgFile = sys.argv[5]
32 unusedReadsFile = sys.argv[6]
33 inputs = string.join(sys.argv[7:],' ')
34 cmdline = 'velvetg %s %s > /dev/null' % (working_dir, inputs)
35 # print >> sys.stderr, cmdline # so will appear as blurb for file
36 try:
37 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
38 returncode = proc.wait()
39 # get stderr, allowing for case where it's very large
40 stderr = ''
41 buffsize = 1048576
42 try:
43 while True:
44 stderr += proc.stderr.read( buffsize )
45 if not stderr or len( stderr ) % buffsize != 0:
46 break
47 except OverflowError:
48 pass
49 if returncode != 0:
50 raise Exception, stderr
51 except Exception, e:
52 stop_err( 'Error running velvetg ' + str( e ) )
53 out = open(contigs,'w')
54 contigs_path = os.path.join(working_dir,'contigs.fa')
55 for line in open( contigs_path ):
56 out.write( "%s" % (line) )
57 out.close()
58 out = open(stats,'w')
59 stats_path = os.path.join(working_dir,'stats.txt')
60 for line in open( stats_path ):
61 out.write( "%s" % (line) )
62 out.close()
63 if LastGraph != 'None':
64 out = open(LastGraph,'w')
65 LastGraph_path = os.path.join(working_dir,'LastGraph')
66 for line in open( LastGraph_path ):
67 out.write( "%s" % (line) )
68 out.close()
69 if afgFile != 'None':
70 out = open(afgFile,'w')
71 afgFile_path = os.path.join(working_dir,'velvet_asm.afg')
72 try:
73 for line in open( afgFile_path ):
74 out.write( "%s" % (line) )
75 except:
76 logging.warn( 'error reading %s' %(afgFile_path))
77 pass
78 out.close()
79 if unusedReadsFile != 'None':
80 out = open(unusedReadsFile,'w')
81 unusedReadsFile_path = os.path.join(working_dir,'UnusedReads.fa')
82 try:
83 for line in open( unusedReadsFile_path ):
84 out.write( "%s" % (line) )
85 except:
86 logging.info( 'error reading %s' %(unusedReadsFile_path))
87 pass
88 out.close()
89
90 if __name__ == "__main__": __main__()