Ejemplo n.º 1
0
 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)
Ejemplo n.º 2
0
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)