|
0
|
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__()
|
