[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | #FIXME: THIS IS 1:1 COPY OF THE SAME FUNCTIONED TOOL - ALLOW REGULAR TOOLS TO MASCARADE AS CONVERTERS |
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| 4 | |
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| 5 | """ |
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| 6 | Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. |
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| 7 | |
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| 8 | usage: %prog input output shift |
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| 9 | """ |
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| 10 | |
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| 11 | import sys, shutil, os |
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| 12 | from galaxy import eggs |
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| 13 | import pkg_resources |
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| 14 | pkg_resources.require( "GeneTrack" ) |
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| 15 | |
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| 16 | from genetrack.scripts import tabs2genetrack |
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| 17 | from genetrack import logger |
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| 18 | |
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| 19 | if __name__ == "__main__": |
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| 20 | import os |
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| 21 | os.environ[ 'LC_ALL' ] = 'C' |
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| 22 | #os.system( 'export' ) |
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| 23 | |
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| 24 | parser = tabs2genetrack.option_parser() |
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| 25 | |
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| 26 | options, args = parser.parse_args() |
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| 27 | |
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| 28 | # uppercase the format |
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| 29 | options.format = options.format.upper() |
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| 30 | |
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| 31 | if options.format not in ('BED', 'GFF'): |
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| 32 | sys.stdout = sys.stderr |
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| 33 | parser.print_help() |
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| 34 | sys.exit(-1) |
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| 35 | |
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| 36 | logger.disable(options.verbosity) |
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| 37 | |
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| 38 | # missing file names |
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| 39 | if not (options.inpname and options.outname and options.format): |
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| 40 | parser.print_help() |
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| 41 | sys.exit(-1) |
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| 42 | else: |
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| 43 | tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ |
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| 44 | format=options.format, shift=options.shift, index=options.index, options=options) |
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