Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data

comparison DiffExpAnal/wrappGSNAP.py @ 0:63799b789162 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author yufei-luo
date Tue, 22 Jan 2013 10:07:03 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:63799b789162
1 #! /usr/bin/env python
2 """
3 Yufei LUO
4 """
5
6
7 import os, sys, subprocess,tempfile
8 from optparse import OptionParser
9
10 def stop_err(msg):
11 sys.stderr.write('%s\n' % msg)
12 sys.exit()
13
14 def __main__():
15 #Parse Command Line
16 description = "GMAP/GSNAP version:2012-12-20."
17 parser = OptionParser(description = description)
18 parser.add_option("-d", "--genomeName", dest="genomeName", help="Define the reference genome name.[compulsory]")
19 parser.add_option("-D", "--workingDir", dest="workingDir", help="Define the directory of writing reference genome index.[compulsory]")
20 parser.add_option("-k", "--kmer", dest="kmer", defaut=12, help="Choose kmer value (<=16), a big kmer value can take more RAM(4Go).[compulsory]")
21 parser.add_option("-i", "--inputFasta", dest="inputFastaFile", help="Reference genome file, fasta format.[compulsory]")
22 parser.add_option("-q", "--inputFastq", dest="inputFastqFile", help="Input fastq file.")
23 parser.add_option("-p", "--pairedEnd", dest="pairedEndFile", defaut=None, help="Input paired-end fastq file.")
24 parser.add_option("-A", "--outputFormat", dest="outputFormat", defaut="sam", help="Choose an output format [sam, goby (need to re-compile with appropriate options)].")
25 (options, args) = parser.parse_args()
26
27 #If workingDir dose not exist, should create before run the job.
28 dir = options.workingdir
29 if not os.path.exists(dir):
30 os.makedirs(dir)
31
32 cmds = []
33 cmd_setup = "gmap_setup -d %s -D %s -k %s %s" % (options.genomeName, options.workingdir, options.kmer, options.inputFastaFile)
34 cmds.append(cmd_setup)
35 cmd_make_coords = "make Makefile.%s coords" % options.genomeName
36 cmds.append(cmd_make_coords)
37 cmd_make_gmapdb = "make Makefile.%s gmapdb" % options.genomeName
38 cmds.append(cmd_make_gmapdb)
39 cmd_make_install = "make Makefile.%s install" % options.genomeName
40 cmds.append(cmd_make_install)
41 cmd_run = "gsnap -d %s -D %s -A %s %s " % (options.genomeName, options.workingdir, options.outputFormat, options.inputFastqFile)
42 if options.pairedEndFile != None:
43 cmd_run += "%s" % options.pairedEndFile
44 cmds.append(cmd_run)
45
46 tmp_files = []
47 for i in range(len(cmds)):
48 try:
49 tmp_out = tempfile.NamedTemporaryFile().name
50 tmp_files.append(tmp_out)
51 tmp_stdout = open(tmp_out, 'wb')
52 tmp_err = tempfile.NamedTemporaryFile().name
53 tmp_files.append(tmp_err)
54 tmp_stderr = open(tmp_err, 'wb')
55 proc = subprocess.Popen(args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr)
56 returncode = proc.wait()
57 tmp_stderr.close()
58 #get stderr, allowing for case where it's very large
59 tmp_stderr = open(tmp_err, 'rb')
60 stderr = ''
61 buffsize = 1048576
62 try:
63 while True:
64 stderr += tmp_stderr.read(buffsize)
65 if not stderr or len(stderr) % buffsize != 0:
66 break
67 except OverflowError:
68 pass
69 tmp_stdout.close()
70 tmp_stderr.close()
71 if returncode != 0:
72 raise Exception, stderr
73 except Exception, e:
74 stop_err('Error in :\n' + str(e))
75
76 for tmp_file in tmp_files:
77 os.remove(tmp_file)
78
79 if __name__=="__main__":__main__()