Mercurial > repos > xuebing > sharplabtool
comparison tools/genetrack/genetrack_peak_prediction.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. | |
| 5 | |
| 6 usage: %prog input output level sigma mode exclusion strand | |
| 7 """ | |
| 8 | |
| 9 import sys | |
| 10 from galaxy import eggs | |
| 11 import pkg_resources | |
| 12 pkg_resources.require( "GeneTrack" ) | |
| 13 | |
| 14 from genetrack.scripts import peakpred | |
| 15 from genetrack import logger | |
| 16 | |
| 17 if __name__ == "__main__": | |
| 18 | |
| 19 parser = peakpred.option_parser() | |
| 20 | |
| 21 options, args = parser.parse_args() | |
| 22 | |
| 23 logger.disable(options.verbosity) | |
| 24 | |
| 25 from genetrack import conf | |
| 26 | |
| 27 # trigger test mode | |
| 28 if options.test: | |
| 29 options.inpname = conf.testdata('test-hdflib-input.gtrack') | |
| 30 options.outname = conf.testdata('predictions.bed') | |
| 31 | |
| 32 # missing input file name | |
| 33 if not options.inpname and not options.outname: | |
| 34 parser.print_help() | |
| 35 else: | |
| 36 print 'Sigma = %s' % options.sigma | |
| 37 print 'Minimum peak = %s' % options.level | |
| 38 print 'Peak-to-peak = %s' % options.exclude | |
| 39 | |
| 40 peakpred.predict(options.inpname, options.outname, options) |