Mercurial > repos > konradpaszkiewicz > oasesoptimiser

annotate oases_optimiser.py @ 0:d35f713f5dc4 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author konradpaszkiewicz
date Tue, 07 Jun 2011 17:09:27 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
1 #!/usr/bin/env python
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
2
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
3 """
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
4 VelvetOptimiser Wrapper
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
5 Adapted from velveth and velvetg tools in Galaxy
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
6 Konrad Paszkiewicz University of Exeter, UK.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
7
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
8 """
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
9 import pkg_resources;
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
10 import logging, os, string, sys, tempfile, glob, shutil, types, urllib
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
11 import shlex, subprocess
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
12 from optparse import OptionParser, OptionGroup
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
13 from stat import *
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
14
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
15
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
16 log = logging.getLogger( __name__ )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
17
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
18 assert sys.version_info[:2] >= ( 2, 4 )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
19
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
20 def stop_err( msg ):
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
21 sys.stderr.write( "%s\n" % msg )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
22 sys.exit()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
23
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
24 def __main__():
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
25 #Parse Command Line
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
26 s = 'oases_optimiser.py: argv = %s\n' % (sys.argv)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
27 #print >> sys.stderr, s # so will appear as blurb for file
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
28 argcnt = len(sys.argv)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
29 starthash = sys.argv[1]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
30 endhash = sys.argv[2]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
31 inputs = sys.argv[3]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
32 contigs = sys.argv[4]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
33 LastGraph = sys.argv[5]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
34 afgFile = sys.argv[6]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
35 unused_reads_fasta = sys.argv[7]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
36 stats = sys.argv[8]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
37 othervelvetgoptions = sys.argv[9]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
38 otheroasesoptions = sys.argv[10]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
39 transcripts = sys.argv[11]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
40 splicingevents = sys.argv[12]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
41 contigordering = sys.argv[13]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
42 #contigs.extra_files_path
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
43
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
44
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
45 working_dir = ''
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
46
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
47 cmdline = '/users/galaxy/galaxyscripts/oases_optimiser.sh %s %s \'%s\' %s %s 2&1>/dev/null' % (starthash, endhash, inputs, othervelvetgoptions, otheroasesoptions)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
48 #print >> sys.stderr, cmdline # so will appear as blurb for file
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
49 try:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
50 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
51 returncode = proc.wait()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
52 # get stderr, allowing for case where it's very large
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
53 stderr = ''
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
54 buffsize = 1048576
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
55 try:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
56 while True:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
57 stderr += proc.stderr.read( buffsize )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
58 if not stderr or len( stderr ) % buffsize != 0:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
59 break
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
60 except OverflowError:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
61 pass
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
62 if returncode != 0:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
63 raise Exception, stderr
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
64 except Exception, e:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
65 stop_err( 'Error running oases_optimiser.py' + str( e ) )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
66 out = open(transcripts,'w')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
67 transcript_path = os.path.join(working_dir,'transcripts.fa')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
68 #print >> sys.stderr, path
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
69 for line in open(transcript_path):
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
70 out.write( "%s" % (line) )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
71 out.close()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
72
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
73 out = open(splicingevents,'w')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
74 path = os.path.join(working_dir,'splicing_events.txt')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
75 #print >> sys.stderr, contigs_path
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
76 for line in open(path ):
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
77 out.write( "%s" % (line) )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
78 out.close()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
79
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
80
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
81
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
82 out = open(contigs,'w')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
83 contigs_path = os.path.join(working_dir,'contigs.fa')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
84 #print >> sys.stderr, contigs_path
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
85 for line in open(contigs_path ):
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
86 out.write( "%s" % (line) )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
87 out.close()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
88 out = open(stats,'w')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
89 stats_path = os.path.join(working_dir,'stats.txt')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
90 for line in open( stats_path ):
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
91 out.write( "%s" % (line) )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
92 out.close()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
93 if LastGraph != 'None':
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
94 out = open(LastGraph,'w')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
95 LastGraph_path = os.path.join(working_dir,'LastGraph')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
96 for line in open( LastGraph_path ):
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
97 out.write( "%s" % (line) )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
98 out.close()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
99 if afgFile != 'None':
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
100 out = open(afgFile,'w')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
101 afgFile_path = os.path.join(working_dir,'oases_asm.afg')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
102 try:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
103 for line in open( afgFile_path ):
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
104 out.write( "%s" % (line) )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
105 except:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
106 logging.warn( 'error reading %s' %(afgFile_path))
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
107 pass
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
108 out.close()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
109 if unused_reads_fasta != 'None':
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
110 out = open(unused_reads_fasta,'w')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
111 unused_reads_fasta_path = os.path.join(working_dir,'UnusedReads.fa')
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
112 try:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
113 for line in open( unused_reads_fasta_path ):
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
114 out.write( "%s" % (line) )
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
115 except:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
116 logging.info( 'error reading %s' %(unused_reads_fasta_path))
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
117 pass
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
118 out.close()
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
119
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
120 if __name__ == "__main__": __main__()