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
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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)