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