[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. |
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| 5 | |
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| 6 | usage: %prog input output level sigma mode exclusion strand |
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| 7 | """ |
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| 8 | |
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| 9 | import sys |
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| 10 | from galaxy import eggs |
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| 11 | import pkg_resources |
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| 12 | pkg_resources.require( "GeneTrack" ) |
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| 13 | |
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| 14 | from genetrack.scripts import peakpred |
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| 15 | from genetrack import logger |
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| 16 | |
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| 17 | if __name__ == "__main__": |
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| 18 | |
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| 19 | parser = peakpred.option_parser() |
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| 20 | |
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| 21 | options, args = parser.parse_args() |
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| 22 | |
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| 23 | logger.disable(options.verbosity) |
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| 24 | |
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| 25 | from genetrack import conf |
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| 26 | |
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| 27 | # trigger test mode |
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| 28 | if options.test: |
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| 29 | options.inpname = conf.testdata('test-hdflib-input.gtrack') |
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| 30 | options.outname = conf.testdata('predictions.bed') |
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| 31 | |
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| 32 | # missing input file name |
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| 33 | if not options.inpname and not options.outname: |
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| 34 | parser.print_help() |
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| 35 | else: |
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| 36 | print 'Sigma = %s' % options.sigma |
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| 37 | print 'Minimum peak = %s' % options.level |
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| 38 | print 'Peak-to-peak = %s' % options.exclude |
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| 39 | |
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| 40 | peakpred.predict(options.inpname, options.outname, options) |
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