Python sort_otu_table Examples

Example #1

File: sort_otu_table.py Project: Sandy4321/FizzyQIIME

def main():
    option_parser, opts, args =\
      parse_command_line_parameters(**script_info)

    otu_table_data = parse_biom_table(open(opts.input_otu_table, 'U'))
    sort_field = opts.sort_field
    mapping_fp = opts.mapping_fp
    sorted_sample_ids_fp = opts.sorted_sample_ids_fp

    if sort_field and mapping_fp:
        mapping_data = parse_mapping_file(open(mapping_fp, 'U'))
        result = sort_otu_table_by_mapping_field(otu_table_data, mapping_data,
                                                 sort_field)
    elif sorted_sample_ids_fp:
        sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp, 'U'))
        result = sort_otu_table(otu_table_data, sorted_sample_ids)
    else:
        result = sort_otu_table(
            otu_table_data, natsort_case_insensitive(otu_table_data.SampleIds))

    # format and write the otu table
    result_str = format_biom_table(result)
    of = open(opts.output_fp, 'w')
    of.write(result_str)
    of.close()

Example #2

File: sort_otu_table.py Project: rob-knight/qiime

def main():
    option_parser, opts, args =\
      parse_command_line_parameters(**script_info)

    otu_table_data = parse_biom_table(open(opts.input_otu_table,'U'))
    sort_field = opts.sort_field
    mapping_fp = opts.mapping_fp
    sorted_sample_ids_fp = opts.sorted_sample_ids_fp
    
    if sort_field and mapping_fp:
        mapping_data = parse_mapping_file(open(mapping_fp,'U'))
        result = sort_otu_table_by_mapping_field(otu_table_data,
                                                 mapping_data,
                                                 sort_field)
    elif sorted_sample_ids_fp:
        sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp,'U'))
        result = sort_otu_table(otu_table_data,
                                sorted_sample_ids)
    else:
        result = sort_otu_table(otu_table_data,
                        natsort_case_insensitive(otu_table_data.SampleIds))
    
    # format and write the otu table
    result_str = format_biom_table(result)
    of = open(opts.output_fp,'w')
    of.write(result_str)
    of.close()

Example #3

    def test_sort_otu_table(self):
        """ sort_otu_table fns as expected """

        actual = sort_otu_table(parse_biom_table_str(self.otu_table1),
                                ['NA','Key','Fing'])
        expected = parse_biom_table_str(self.age_sorted_otu_table1)
        self.assertEqual(actual, expected)

Example #4

File: sort_otu_table.py Project: Ecogenomics/FrankenQIIME

def main():
    option_parser, opts, args =\
      parse_command_line_parameters(**script_info)

    otu_table_data = parse_otu_table(open(opts.input_otu_table,'U'))
    sort_field = opts.sort_field
    mapping_fp = opts.mapping_fp
    sorted_sample_ids_fp = opts.sorted_sample_ids_fp
    
    if sort_field and mapping_fp:
        mapping_data = parse_mapping_file(open(mapping_fp,'U'))
        result = sort_otu_table_by_mapping_field(otu_table_data,
                                                 mapping_data,
                                                 sort_field)
    elif sorted_sample_ids_fp:
        sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp,'U'))
        result = sort_otu_table(otu_table_data,
                                sorted_sample_ids)
    else:
        parser.error("must provide either --sort_field and --mapping_fp OR --sorted_sample_ids_fp")

    # format and write the otu table
    result_str = format_otu_table(result[0],result[1],result[2],result[3])
    of = open(opts.output_fp,'w')
    of.write(result_str)
    of.close()

Example #5

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    otu_table_data = load_table(opts.input_otu_table)
    sort_field = opts.sort_field
    mapping_fp = opts.mapping_fp
    sorted_sample_ids_fp = opts.sorted_sample_ids_fp

    if sort_field and mapping_fp:
        mapping_data = parse_mapping_file(open(mapping_fp, 'U'))
        result = sort_otu_table_by_mapping_field(otu_table_data, mapping_data,
                                                 sort_field)
    elif sorted_sample_ids_fp:
        sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp, 'U'))
        result = sort_otu_table(otu_table_data, sorted_sample_ids)
    else:
        result = sort_otu_table(otu_table_data,
                                natsort_case_insensitive(otu_table_data.ids()))

    write_biom_table(result, opts.output_fp)

Example #6

File: sort_otu_table.py Project: Springbudder/qiime

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    otu_table_data = load_table(opts.input_otu_table)
    sort_field = opts.sort_field
    mapping_fp = opts.mapping_fp
    sorted_sample_ids_fp = opts.sorted_sample_ids_fp

    if sort_field and mapping_fp:
        mapping_data = parse_mapping_file(open(mapping_fp, 'U'))
        result = sort_otu_table_by_mapping_field(otu_table_data, mapping_data,
                                                 sort_field)
    elif sorted_sample_ids_fp:
        sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp, 'U'))
        result = sort_otu_table(otu_table_data,
                                sorted_sample_ids)
    else:
        result = sort_otu_table(otu_table_data,
            natsort_case_insensitive(otu_table_data.ids()))

    write_biom_table(result, opts.output_fp)

Example #7

File: test_sort.py Project: Ecogenomics/FrankenQIIME

    def test_sort_otu_table(self):
        """ sort_otu_table fns as expected """

        actual = sort_otu_table(parse_otu_table(self.otu_table1),
                                ['NA','Key','Fing'])
        expected = parse_otu_table(self.age_sorted_otu_table1)
        # sample ids match expected
        self.assertEqual(actual[0],expected[0])
        # otu ids match expected
        self.assertEqual(actual[1],expected[1])
        # otu data match expected
        self.assertEqual(actual[2],expected[2])
        # taxa match expected
        self.assertEqual(actual[3],expected[3])