Python sample_mapping_to_biom_table Examples

Example #1

File: test_sample_id_map_otu_table_conversion.py Project: elisemorrison/FastUnifrac

    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())

Example #2

    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())

Example #3

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))

Example #4

File: convert_sample_id_map_to_otu_table.py Project: elisemorrison/FastUnifrac

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))