rv, err = self.execute(params) self.assertEqual(0, rv) self.assertFilesEqual(expected_file, output_file, filter_regex="##fileDate=") def test_sample2_none_second(self): both_samples = self.inputFiles("vcf-merge/consensus/merge-S1-S2.vcf")[0] sample2_none = self.inputFiles("vcf-merge/consensus/merge-S2-none.vcf")[0] sample2_empty = self.inputFiles("vcf-merge/consensus/merge-S2-empty.vcf")[0] expected_file = self.inputFiles("vcf-merge/consensus/expected-S1-S2_S2-none.vcf")[0] output_file = self.tempFile("output.vcf") base_params = [ "vcf-merge", "-s", "-R 1.0,FILT,FILT", "-o", output_file ] equivalent_inputs = [ [both_samples, sample2_none], [both_samples, sample2_empty] ] base_params = [ "vcf-merge", "-s", "-R 1.0,FILT,FILT", "-o", output_file ] for inputs in equivalent_inputs: params = base_params + inputs rv, err = self.execute(params) self.assertEqual(0, rv) self.assertFilesEqual(expected_file, output_file, filter_regex="##fileDate=") if __name__ == "__main__": main()
] rv, err = self.execute(params) self.assertEqual(0, rv) self.assertFilesEqual(expected_file, output_file, filter_regex="##fileDate=") def test_vcf_merge_per_alt_list(self): merge_strategy_file = self.tempFile("strategy.ms") open(merge_strategy_file, "w").write("info.CALLER=per-alt-delimited-list") input_files = sorted( self.inputFiles("vcf-merge/merge-per-alt-list-[12].vcf")) self.assertEqual(2, len(input_files)) expected_file = self.inputFiles( "vcf-merge/expected-merge-per-alt-list.vcf")[0] output_file = self.tempFile("output.vcf") params = ["vcf-merge", "-M", merge_strategy_file, "-o", output_file ] + input_files rv, err = self.execute(params) self.assertEqual(0, rv) self.assertFilesEqual(expected_file, output_file, filter_regex="##fileDate=") if __name__ == "__main__": main()
import mdl import xmltest _parser = argparse.ArgumentParser() _subparsers = _parser.add_subparsers(dest='cmd') if __name__ == '__main__': buildsystem_parser = buildsystem.init_parser(_subparsers) integrationtest_parser = integrationtest.init_parser(_subparsers) installer_parser = installer.init_parser(_subparsers) odbhelper_parser = odb.init_parser(_subparsers) mdl_parser = mdl.init_parser(_subparsers) xmltest_parser = xmltest.init_parser(_subparsers) args = _parser.parse_args() if args.cmd is None: _parser.print_help() elif args.cmd == 'buildsystem': buildsystem.main(args) elif args.cmd == 'integrationtest': integrationtest.main(args) elif args.cmd == 'installer': installer.main(args) elif args.cmd == 'odb': odb.main(args) elif args.cmd == 'mdl': mdl.main(args) elif args.cmd == 'xmltest': xmltest.main(args)