def test_split_mapping_file_on_field(self): """ split_mapping_file_on_field functions as expected with valid input """ actual = sorted( split_mapping_file_on_field(self.mapping_f1, 'Treatment')) self.mapping_exp.sort() self.assertEqual(actual, self.mapping_exp)
def test_split_mapping_file_on_field(self): """ split_mapping_file_on_field functions as expected with valid input """ actual = list(split_mapping_file_on_field(self.mapping_f1,'Treatment')) actual.sort() self.mapping_exp.sort() self.assertEqual(actual,self.mapping_exp)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) otu_table_fp = opts.otu_table_fp mapping_fp = opts.mapping_fp mapping_field = opts.mapping_field output_dir = opts.output_dir # column_rename_ids = opts.column_rename_ids # include_repeat_cols = opts.include_repeat_cols create_dir(output_dir) # split mapping file mapping_f = open(mapping_fp, 'U') for fp_str, sub_mapping_s in split_mapping_file_on_field(mapping_f, mapping_field): mapping_output_fp = join(output_dir, 'mapping_%s.txt' % fp_str) open(mapping_output_fp, 'w').write(sub_mapping_s) # split otu table otu_table_base_name = splitext(split(otu_table_fp)[1])[0] mapping_f = open(mapping_fp, 'U') otu_table = load_table(otu_table_fp) try: for fp_str, sub_otu_table_s in split_otu_table_on_sample_metadata( otu_table, mapping_f, mapping_field): otu_table_output_fp = join(output_dir, '%s_%s.biom' % ( otu_table_base_name, fp_str)) write_biom_table(sub_otu_table_s, otu_table_output_fp) except OTUTableSplitError as e: option_parser.error(e)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) otu_table_fp = opts.otu_table_fp mapping_fp = opts.mapping_fp mapping_field = opts.mapping_field output_dir = opts.output_dir # column_rename_ids = opts.column_rename_ids # include_repeat_cols = opts.include_repeat_cols create_dir(output_dir) # split mapping file mapping_f = open(mapping_fp, 'U') for fp_str, sub_mapping_s in split_mapping_file_on_field(mapping_f, mapping_field): mapping_output_fp = join(output_dir, 'mapping_%s.txt' % fp_str) open(mapping_output_fp, 'w').write(sub_mapping_s) # split otu table otu_table_base_name = splitext(split(otu_table_fp)[1])[0] mapping_f = open(mapping_fp, 'U') otu_table_f = open(otu_table_fp, 'U') for fp_str, sub_otu_table_s in split_otu_table_on_sample_metadata( otu_table_f, mapping_f, mapping_field): otu_table_output_fp = join( output_dir, '%s_%s.biom' % (otu_table_base_name, fp_str)) open(otu_table_output_fp, 'w').write(sub_otu_table_s)