def test_get_reference_tree(self): fp = get_reference_tree() self.assertIn(os.path.join('gg_13_8_otus', 'trees', '97_otus.tree'), fp) self.assertTrue(os.path.isfile(fp)) self.assertTrue(os.path.isabs(fp)) with open(fp, 'rb') as f: md5 = safe_md5(f).hexdigest() self.assertEqual(md5, 'b7e76593bce82913af1cfb06edf15732')
def test_get_reference_tree(self): fp = get_reference_tree() self.assertIn( os.path.join('gg_13_8_otus', 'trees', '97_otus.tree'), fp) self.assertTrue(os.path.isfile(fp)) self.assertTrue(os.path.isabs(fp)) with open(fp, 'rb') as f: md5 = safe_md5(f).hexdigest() self.assertEqual(md5, 'b7e76593bce82913af1cfb06edf15732')
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) verbose = opts.verbose input_fp = opts.input_fp reference_fp = opts.reference_fp taxonomy_fp = opts.taxonomy_fp output_dir = opts.output_dir verbose = opts.verbose print_only = opts.print_only assign_taxonomy = opts.assign_taxonomy if opts.suppress_taxonomy_assignment: assign_taxonomy = False taxonomy_fp = None parallel = opts.parallel # No longer checking that jobs_to_start > 2, but # commenting as we may change our minds about this. # if parallel: raise_error_on_parallel_unavailable() if opts.parameter_fp: try: parameter_f = open(opts.parameter_fp, 'U') except IOError: raise IOError("Can't open parameters file (%s). Does it exist? Do you have read access?" % opts.parameter_fp) params = parse_qiime_parameters(parameter_f) parameter_f.close() else: params = parse_qiime_parameters([]) # empty list returns empty defaultdict for now jobs_to_start = opts.jobs_to_start default_jobs_to_start = qiime_config['jobs_to_start'] validate_and_set_jobs_to_start(params, jobs_to_start, default_jobs_to_start, parallel, option_parser) if print_only: command_handler = print_commands else: command_handler = call_commands_serially try: makedirs(output_dir) except OSError: if opts.force: pass else: option_parser.error("Output directory already exists. Please choose" " a different directory, or force overwrite with -f.") if verbose: status_update_callback = print_to_stdout else: status_update_callback = no_status_updates run_pick_closed_reference_otus( input_fp, reference_fp, output_dir, taxonomy_fp, assign_taxonomy=assign_taxonomy, command_handler=command_handler, params=params, qiime_config=qiime_config, parallel=parallel, status_update_callback=status_update_callback) if get_reference_sequences() == reference_fp: reference_tree_fp = get_reference_tree() fn = basename(reference_tree_fp) copyfile(reference_tree_fp, join(output_dir, fn))
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) verbose = opts.verbose input_fp = opts.input_fp reference_fp = opts.reference_fp taxonomy_fp = opts.taxonomy_fp output_dir = opts.output_dir verbose = opts.verbose print_only = opts.print_only assign_taxonomy = opts.assign_taxonomy if opts.suppress_taxonomy_assignment: assign_taxonomy = False taxonomy_fp = None parallel = opts.parallel # No longer checking that jobs_to_start > 2, but # commenting as we may change our minds about this. # if parallel: raise_error_on_parallel_unavailable() if opts.parameter_fp: try: parameter_f = open(opts.parameter_fp, 'U') except IOError: raise IOError( "Can't open parameters file (%s). Does it exist? Do you have read access?" % opts.parameter_fp) params = parse_qiime_parameters(parameter_f) parameter_f.close() else: params = parse_qiime_parameters([]) # empty list returns empty defaultdict for now jobs_to_start = opts.jobs_to_start default_jobs_to_start = qiime_config['jobs_to_start'] validate_and_set_jobs_to_start(params, jobs_to_start, default_jobs_to_start, parallel, option_parser) if print_only: command_handler = print_commands else: command_handler = call_commands_serially try: makedirs(output_dir) except OSError: if opts.force: pass else: option_parser.error( "Output directory already exists. Please choose" " a different directory, or force overwrite with -f.") if verbose: status_update_callback = print_to_stdout else: status_update_callback = no_status_updates run_pick_closed_reference_otus( input_fp, reference_fp, output_dir, taxonomy_fp, assign_taxonomy=assign_taxonomy, command_handler=command_handler, params=params, qiime_config=qiime_config, parallel=parallel, status_update_callback=status_update_callback) if get_reference_sequences() == reference_fp: reference_tree_fp = get_reference_tree() fn = basename(reference_tree_fp) copyfile(reference_tree_fp, join(output_dir, fn))