Mercurial > repos > saket-choudhary > eqtl_tools

annotate panama_run.py @ 7:bef89654259a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
temp commit
author Saket Choudhary<saketkc@gmail.com>
date Fri, 21 Jun 2013 10:56:27 +0530
parents 7265ecc0f879
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
1 #!/usr/bin/env python
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
2 """
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
3 Run panama on expression and snp data
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
4 usage: panama_run.py [options]
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
5 --exp_data: Expression data CSV file
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
6 --snp_data: SNP data file
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
7 --output1: Output CSV dataset
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
8 """
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
9
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
10 import optparse, os, sys, subprocess, tempfile, shutil
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
11 from galaxy import eggs
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
12 import pkg_resources; pkg_resources.require( "bx-python" )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
13 from bx.cookbook import doc_optparse
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
14 from galaxy import util
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
15
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
16 def stop_err( msg ):
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
17 sys.stderr.write( '%s\n' % msg )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
18 sys.exit()
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
19
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
20
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
21
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
22 def __main__():
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
23 #Parse Command Line
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
24 parser = optparse.OptionParser()
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
25 parser.add_option( '', '--exp_data', dest='exp_data', help='The input Expression dataset')
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
26 parser.add_option( '', '--snp_data', dest='snp_data', help='The input snp dataset' )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
27 parser.add_option( '', '--output1', dest='output1', help='The output CSV dataset' )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
28 ( options, args ) = parser.parse_args()
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
29
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
30 try:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
31 tmp_dir = tempfile.mkdtemp()
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
32 panama_output_file_name = os.path.join(tmp_dir, "PANAMA_results.csv")
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
33 command = 'panama %s %s -d %s' %(options.exp_data,options.snp_data,tmp_dir)
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
34 print command
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
35 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
36 tmp_stderr = open( tmp, 'wb' )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
37 proc = subprocess.Popen( args=command, shell=True, stderr=tmp_stderr.fileno() )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
38 returncode = proc.wait()
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
39 tmp_stderr.close()
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
40 # get stderr, allowing for case where it's very large
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
41 tmp_stderr = open( tmp, 'rb' )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
42 stderr = ''
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
43 buffsize = 1048576
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
44 try:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
45 while True:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
46 stderr += tmp_stderr.read( buffsize )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
47 if not stderr or len( stderr ) % buffsize != 0:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
48 break
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
49 except OverflowError:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
50 pass
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
51 tmp_stderr.close()
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
52 if returncode != 0:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
53 raise Exception, stderr
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
54 except Exception, e:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
55 #clean up temp files
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
56 print e
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
57 if os.path.exists( tmp_dir ):
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
58 shutil.rmtree( tmp_dir )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
59 stop_err( 'Error opening panama')
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
60 # Move tmp_aligns_file_name to our output dataset location
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
61 shutil.move( panama_output_file_name, options.output1 )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
62 #clean up temp files
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
63 if os.path.exists( tmp_dir ):
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
64 shutil.rmtree( tmp_dir )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
65 # check that there are results in the output file
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
66 if os.path.getsize( options.output1 ) > 0:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
67 sys.stdout.write( 'PANAM results generated' )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
68 else:
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
69 stop_err( 'Error generating PANAMA results' )
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
70
7265ecc0f879 Moving the files to proper hiererachy levels
Saket Choudhary<saketkc@gmail.com>
parents:
diff changeset
71 if __name__=="__main__": __main__()