Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/ComputeCoverage.py @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | 769e306b7933 |
| children |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
|---|---|
| 128 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of the first file [compulsory] [format: transcript file format]") | 128 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of the first file [compulsory] [format: transcript file format]") |
| 129 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input reference file [compulsory] [format: file in transcript format given by -f]") | 129 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input reference file [compulsory] [format: file in transcript format given by -f]") |
| 130 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of the second file [compulsory] [format: transcript file format]") | 130 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of the second file [compulsory] [format: transcript file format]") |
| 131 parser.add_option("-t", "--introns", dest="introns", action="store_true", default=False, help="also include introns [format: boolean] [default: false]") | 131 parser.add_option("-t", "--introns", dest="introns", action="store_true", default=False, help="also include introns [format: boolean] [default: false]") |
| 132 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [format: output file in GFF3 format]") | 132 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [format: output file in GFF3 format]") |
| 133 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", type="int", help="trace level [default: 1] [format: int]") | 133 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]") |
| 134 (options, args) = parser.parse_args() | 134 (options, args) = parser.parse_args() |
| 135 | 135 |
| 136 computer = CoverageComputer(options.verbosity) | 136 computer = CoverageComputer(options.verbosity) |
| 137 computer.setInputQueryFile(options.inputFileName1, options.format1) | 137 computer.setInputQueryFile(options.inputFileName1, options.format1) |
| 138 computer.setInputReferenceFile(options.inputFileName2, options.format2) | 138 computer.setInputReferenceFile(options.inputFileName2, options.format2) |