Mercurial > repos > xuebing > sharplabtool

comparison tools/next_gen_conversion/solid_to_fastq.py @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2
3 """
4 Converts SOLiD data to Sanger FASTQ format.
5
6 usage: %prog [options]
7 -i, --input1=i: Forward reads file
8 -q, --input2=q: Forward qual file
9 -I, --input3=I: Reverse reads file
10 -Q, --input4=Q: Reverse qual file
11 -o, --output1=o: Forward output
12 -r, --output2=r: Reverse output
13
14 usage: %prog forward_reads_file forwards_qual_file reverse_reads_file(or_None) reverse_qual_file(or_None) output_file ouptut_id output_dir
15 """
16
17 import os, sys, tempfile
18 from galaxy import eggs
19 import pkg_resources; pkg_resources.require( "bx-python" )
20 from bx.cookbook import doc_optparse
21
22 def stop_err( msg ):
23 sys.stderr.write( "%s\n" % msg )
24 sys.exit()
25
26 def replaceNeg1(fin, fout):
27 line = fin.readline()
28 while line.strip():
29 fout.write(line.replace('-1', '1'))
30 line = fin.readline()
31 fout.seek(0)
32 return fout
33
34 def __main__():
35 #Parse Command Line
36 options, args = doc_optparse.parse( __doc__ )
37 # common temp file setup
38 tmpf = tempfile.NamedTemporaryFile() #forward reads
39 tmpqf = tempfile.NamedTemporaryFile()
40 tmpqf = replaceNeg1(file(options.input2,'r'), tmpqf)
41 # if paired-end data (have reverse input files)
42 if options.input3 != "None" and options.input4 != "None":
43 tmpr = tempfile.NamedTemporaryFile() #reverse reads
44 # replace the -1 in the qualities file
45 tmpqr = tempfile.NamedTemporaryFile()
46 tmpqr = replaceNeg1(file(options.input4,'r'), tmpqr)
47 cmd1 = "%s/bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s 2>&1" %(os.path.split(sys.argv[0])[0], tmpf.name, tmpr.name, options.input1, tmpqf.name, options.input3, tmpqr.name)
48 try:
49 os.system(cmd1)
50 os.system('gunzip -c %s >> %s' %(tmpf.name,options.output1))
51 os.system('gunzip -c %s >> %s' %(tmpr.name,options.output2))
52 except Exception, eq:
53 stop_err("Error converting data to fastq format.\n" + str(eq))
54 tmpr.close()
55 tmpqr.close()
56 # if single-end data
57 else:
58 cmd1 = "%s/bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s 2>&1" % (os.path.split(sys.argv[0])[0], tmpf.name, None, options.input1, tmpqf.name, None, None)
59 try:
60 os.system(cmd1)
61 os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1))
62 except Exception, eq:
63 stop_err("Error converting data to fastq format.\n" + str(eq))
64 tmpqf.close()
65 tmpf.close()
66 sys.stdout.write('converted SOLiD data')
67
68 if __name__=="__main__": __main__()