def test_compute_min_alignment_length(self): """compute_min_alignment_length: returns n std devs below mean seq len """ self.assertEqual(compute_min_alignment_length(\ self.min_length_computation_seqs),16) self.assertEqual(compute_min_alignment_length(\ self.min_length_computation_seqs,0.60),13)
def test_compute_min_alignment_length(self): """compute_min_alignment_length: returns n std devs below mean seq len """ self.assertEqual(compute_min_alignment_length( self.min_length_computation_seqs), 16) self.assertEqual(compute_min_alignment_length( self.min_length_computation_seqs, 0.60), 13)
def _precommand_initiation(self,input_fp,output_dir,working_dir,params): if not params['blast_db']: # Build the blast database from the reference_seqs_fp -- all procs # will then access one db rather than create one per proc blast_db, db_files_to_remove = \ build_blast_db_from_fasta_path(params['template_fp']) self.files_to_remove += db_files_to_remove params['blast_db'] = blast_db if params['min_length'] < 0: params['min_length'] = compute_min_alignment_length(\ open(input_fp,'U'))
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) if opts.min_percent_id <= 1.0: opts.min_percent_id *= 100 if not (1.0 <= opts.min_percent_id <= 100.0): option_parser.error('Minimum percent sequence identity must be' + ' between 1.0 and 100.0: %2.2f' % opts.min_percent_id) if not opts.template_fp and opts.alignment_method == 'pynast': option_parser.error( 'PyNAST requires a template alignment to be passed via -t') input_seqs_filepath = opts.input_fasta_fp alignment_method = opts.alignment_method output_dir = opts.output_dir or alignment_method + '_aligned' create_dir(output_dir, fail_on_exist=False) # compute the minimum alignment length if a negative value was # provided (the default) min_length = opts.min_length if min_length < 0: min_length = compute_min_alignment_length( open(input_seqs_filepath, 'U')) fpath, ext = splitext(input_seqs_filepath) input_dir, fname = split(fpath) result_path = output_dir + '/' + fname + "_aligned.fasta" log_path = output_dir + '/' + fname + "_log.txt" failure_path = output_dir + '/' + fname + "_failures.fasta" if alignment_method in alignment_method_constructors: # try/except was causing problems here, so replacing with # an explicit check # define the aligner params aligner_constructor =\ alignment_method_constructors[alignment_method] aligner_type = alignment_method params = {'min_len': min_length, 'min_pct': opts.min_percent_id, 'template_filepath': opts.template_fp, 'blast_db': opts.blast_db, 'pairwise_alignment_method': opts.pairwise_alignment_method} # build the aligner object aligner = aligner_constructor(params) # apply the aligner aligner(input_seqs_filepath, result_path=result_path, log_path=log_path, failure_path=failure_path) else: # define the aligner params aligner = CogentAligner({ 'Module': alignment_module_names.get(alignment_method, 'Unknown'), 'Method': alignment_method }) if alignment_method == "muscle": if opts.muscle_max_memory is not None: aligner.Params["-maxmb"] = str(opts.muscle_max_memory) # build the aligner aligner_type = 'Cogent' # apply the aligner aligner(result_path, seq_path=input_seqs_filepath, log_path=log_path)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) if opts.min_percent_id <= 1.0: opts.min_percent_id *= 100 if not (1.0 <= opts.min_percent_id <= 100.0): option_parser.error('Minimum percent sequence identity must be' + ' between 1.0 and 100.0: %2.2f' % opts.min_percent_id) if not opts.template_fp and opts.alignment_method == 'pynast': option_parser.error( 'PyNAST requires a template alignment to be passed via -t') input_seqs_filepath = opts.input_fasta_fp alignment_method = opts.alignment_method output_dir = opts.output_dir or alignment_method + '_aligned' create_dir(output_dir, fail_on_exist=False) # compute the minimum alignment length if a negative value was # provided (the default) min_length = opts.min_length if min_length < 0: min_length = compute_min_alignment_length( open(input_seqs_filepath, 'U')) fpath, ext = splitext(input_seqs_filepath) input_dir, fname = split(fpath) result_path = output_dir + '/' + fname + "_aligned.fasta" log_path = output_dir + '/' + fname + "_log.txt" failure_path = output_dir + '/' + fname + "_failures.fasta" if alignment_method in alignment_method_constructors: # try/except was causing problems here, so replacing with # an explicit check # define the aligner params aligner_constructor =\ alignment_method_constructors[alignment_method] aligner_type = alignment_method params = { 'min_len': min_length, 'min_pct': opts.min_percent_id, 'template_filepath': opts.template_fp, 'blast_db': opts.blast_db, 'pairwise_alignment_method': opts.pairwise_alignment_method } # build the aligner object aligner = aligner_constructor(params) # apply the aligner aligner(input_seqs_filepath, result_path=result_path, log_path=log_path, failure_path=failure_path) else: # define the aligner params aligner = CogentAligner({ 'Module': alignment_module_names.get(alignment_method, 'Unknown'), 'Method': alignment_method }) if alignment_method == "muscle": if opts.muscle_max_memory is not None: aligner.Params["-maxmb"] = str(opts.muscle_max_memory) # build the aligner aligner_type = 'Cogent' # apply the aligner aligner(result_path, seq_path=input_seqs_filepath, log_path=log_path)
def _precommand_initiation(self, input_fp, output_dir, working_dir, params): if params['min_length'] < 0: params['min_length'] = compute_min_alignment_length( open(input_fp, 'U'))
def _precommand_initiation( self, input_fp, output_dir, working_dir, params): if params['min_length'] < 0: params['min_length'] = compute_min_alignment_length( open(input_fp, 'U'))