Mercurial > repos > xuebing > sharplabtool

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

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2
3 """
4 Performs various conversions around Sanger FASTQ data
5
6 usage: %prog [options]
7 -c, --command=c: Command to run
8 -i, --input=i: Input file to be converted
9 -o, --outputFastqsanger=o: FASTQ Sanger converted output file for sol2std
10 -s, --outputFastqsolexa=s: FASTQ Solexa converted output file
11 -f, --outputFasta=f: FASTA converted output file
12
13 usage: %prog command input_file output_file
14 """
15
16 import os, sys, tempfile
17 from galaxy import eggs
18 import pkg_resources; pkg_resources.require( "bx-python" )
19 from bx.cookbook import doc_optparse
20
21 def stop_err( msg ):
22 sys.stderr.write( "%s\n" % msg )
23 sys.exit()
24
25 def __main__():
26 #Parse Command Line
27 options, args = doc_optparse.parse( __doc__ )
28
29 cmd = "fq_all2std.pl %s %s > %s"
30 if options.command == 'sol2std':
31 cmd = cmd % (options.command, options.input, options.outputFastqsanger)
32 elif options.command == 'std2sol':
33 cmd = cmd % (options.command, options.input, options.outputFastqsolexa)
34 elif options.command == 'fq2fa':
35 cmd = cmd % (options.command, options.input, options.outputFasta)
36 try:
37 os.system(cmd)
38 except Exception, eq:
39 stop_err("Error converting data format.\n" + str(eq))
40
41 if __name__=="__main__": __main__()