def test_generate_most_wanted_list(self): """Functions correctly using standard valid input data.""" generate_most_wanted_list(self.otu_table_f.name, self.rep_set_f.name, self.ref_seqs_f.name, self.mapping_f.name, self.grouping_category, self.output_dir, self.top_n) obs_txt_f = open(join(self.output_dir, 'top_%d_most_wanted_otus.txt' % self.top_n), 'U') obs_txt = obs_txt_f.read() obs_txt_f.close() self.assertEqual(obs_txt, exp_txt)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) if opts.print_only: command_handler = print_commands else: command_handler = call_commands_serially if opts.verbose: status_update_callback = print_to_stdout else: status_update_callback = no_status_updates generate_most_wanted_list(opts.output_dir, opts.otu_table_fp, opts.rep_set_fp, opts.gg_fp, opts.nt_fp, opts.mapping_fp, opts.mapping_category, opts.top_n, opts.min_abundance, opts.max_abundance, opts.min_categories, opts.max_gg_similarity, opts.e_value, opts.word_size, opts.jobs_to_start, command_handler, status_update_callback, opts.force)