def test_sample_mapping_to_biom_table(self): """sample_mapping_to_biom_table works""" lines = self.SampleMapping actual = sample_mapping_to_biom_table(lines) exp = table_factory(array([[3.,0.,2.],[1.,2.,0.]]), ['sample1','sample2','sample3'], ['OTU1','OTU2']) self.assertEqual(actual.sortBySampleId(), exp.sortBySampleId()) lines = self.SampleMappingNoMIENS actual = sample_mapping_to_biom_table(lines) exp = table_factory(array([[3.,0.,2.],[1.,2.,0.]]), ['sample.1','sample.2','sample.3'], ['OTU1','OTU2']) self.assertEqual(actual.sortBySampleId(), exp.sortBySampleId())
def test_sample_mapping_to_biom_table(self): """sample_mapping_to_biom_table works""" lines = self.SampleMapping actual = sample_mapping_to_biom_table(lines) exp = table_factory(array([[3., 0., 2.], [1., 2., 0.]]), ['sample1', 'sample2', 'sample3'], ['OTU1', 'OTU2']) self.assertEqual(actual.sortBySampleId(), exp.sortBySampleId()) lines = self.SampleMappingNoMIENS actual = sample_mapping_to_biom_table(lines) exp = table_factory(array([[3., 0., 2.], [1., 2., 0.]]), ['sample.1', 'sample.2', 'sample.3'], ['OTU1', 'OTU2']) self.assertEqual(actual.sortBySampleId(), exp.sortBySampleId())
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) sample_mapping_fp = opts.sample_mapping_fp output_fp = opts.output_fp verbose = opts.verbose sample_mapping_file = open(sample_mapping_fp, 'U') result = sample_mapping_to_biom_table(sample_mapping_file) open(output_fp, 'w').write(format_biom_table(result))
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) sample_mapping_fp = opts.sample_mapping_fp output_fp = opts.output_fp verbose = opts.verbose sample_mapping_file = open(sample_mapping_fp, 'U') result = sample_mapping_to_biom_table(sample_mapping_file) open(output_fp, 'w').write(format_biom_table(result))