def test_parallel_align_seqs_pynast(self): """ parallel_align_seqs_pynast functions as expected """ params = { 'min_percent_id': 0.75, 'min_length': 15, 'template_fp': self.template_fp, 'pairwise_alignment_method': 'uclust', 'blast_db': None } app = ParallelAlignSeqsPyNast() r = app(self.inseqs1_fp, self.test_out, params, job_prefix='PTEST', poll_directly=True, suppress_submit_jobs=False) # confirm that the total number of output sequences equals the total # number of input sequences num_input_seqs = count_seqs_in_filepaths([self.inseqs1_fp])[1] num_template_seqs = count_seqs_in_filepaths([self.template_fp])[1] num_output_seqs = \ count_seqs_in_filepaths(glob(join(self.test_out, '*fasta')))[1] \ - num_input_seqs - num_template_seqs self.assertEqual(num_input_seqs, num_output_seqs)
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) suppress_errors = opts.suppress_errors input_fps = [] for e in opts.input_fps.split(','): input_fps.extend(glob(e)) input_fps = set(input_fps) if len(input_fps) == 0: option_parser.error(\ "No filepaths match pattern(s) passed via -i: %s" % ''.join(opts.input_fps)) output_fp = opts.output_fp count_data, total, inaccessible_filepaths = count_seqs_in_filepaths( input_fps) r = format_output(count_data, total, inaccessible_filepaths, suppress_errors) if opts.output_fp: f = open(output_fp, 'w') f.write(r) f.close() else: print r
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) suppress_errors = opts.suppress_errors input_fps = opts.input_fps output_fp = opts.output_fp count_data, total, inaccessible_filepaths = count_seqs_in_filepaths(input_fps) r = format_output(count_data, total, inaccessible_filepaths, suppress_errors) if opts.output_fp: f = open(output_fp,'w') f.write(r) f.close() else: print r
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) suppress_errors = opts.suppress_errors input_fps = [] for e in opts.input_fps.split(','): input_fps.extend(glob(e)) input_fps = set(input_fps) if len(input_fps) == 0: option_parser.error(\ "No filepaths match pattern(s) passed via -i: %s" % ''.join(opts.input_fps)) output_fp = opts.output_fp count_data, total, inaccessible_filepaths = count_seqs_in_filepaths(input_fps) r = format_output(count_data, total, inaccessible_filepaths, suppress_errors) if opts.output_fp: f = open(output_fp,'w') f.write(r) f.close() else: print r