def main(): option_parser, opts, args =\ parse_command_line_parameters(suppress_verbose=True, **script_info) mapping_fp = opts.mapping_fp has_barcodes = not opts.not_barcoded variable_len_barcodes = opts.variable_len_barcodes output_dir = opts.output_dir + "/" char_replace = opts.char_replace verbose = opts.verbose disable_primer_check = opts.disable_primer_check added_demultiplex_field = opts.added_demultiplex_field suppress_html = opts.suppress_html # Create output directory, check path/access to mapping file create_dir(output_dir) # Test for valid replacement characters valid_replacement_chars = digits + letters + "_" + "." if char_replace not in valid_replacement_chars: option_parser.error('-c option requires alphanumeric, period, or ' + 'underscore character.') if len(char_replace) != 1: option_parser.error('-c parameter must be a single character.') check_mapping_file(mapping_fp, output_dir, has_barcodes, char_replace, verbose, variable_len_barcodes, disable_primer_check, added_demultiplex_field, suppress_html)
def main(): option_parser, opts, args =\ parse_command_line_parameters(suppress_verbose=True, **script_info) mapping_fp = opts.mapping_fp has_barcodes = not opts.not_barcoded variable_len_barcodes = opts.variable_len_barcodes output_dir = opts.output_dir + "/" char_replace = opts.char_replace verbose = opts.verbose disable_primer_check = opts.disable_primer_check added_demultiplex_field = opts.added_demultiplex_field # Create output directory, check path/access to mapping file create_dir(output_dir) # Test for valid replacement characters valid_replacement_chars = digits + letters + "_" + "." if char_replace not in valid_replacement_chars: option_parser.error('-c option requires alphanumeric, period, or '+\ 'underscore character.') if len(char_replace) != 1: option_parser.error('-c parameter must be a single character.') check_mapping_file(mapping_fp, output_dir, has_barcodes, char_replace,\ verbose, variable_len_barcodes, disable_primer_check, added_demultiplex_field)
def main(): option_parser, opts, args =\ parse_command_line_parameters(suppress_verbose=True, **script_info) infile_name = opts.map_fname has_barcodes = not opts.not_barcoded output_dir = opts.output_dir char_replace = opts.char_replace var_len_barcodes = opts.variable_len_barcodes verbose = opts.verbose disable_primer_check = opts.disable_primer_check added_demultiplex_field = opts.added_demultiplex_field valid_replacement_chars=digits+letters+"_" if char_replace not in valid_replacement_chars: option_parser.error('-c option requires alphanumeric or '+\ 'underscore character') if len(char_replace) != 1: option_parser.error('-c parameter must be a single character.') check_mapping_file(infile_name, output_dir, has_barcodes, char_replace,\ verbose, var_len_barcodes, disable_primer_check, added_demultiplex_field)