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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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