# Subparser for conversion of SRA headers parser_sra = subparsers.add_parser('sra', parents=[parser_parent], formatter_class=CommonHelpFormatter, help='''Converts NCBI SRA sequence headers.''') parser_sra.set_defaults(convert_func=convertSRAHeader) return parser if __name__ == '__main__': """ Parses command line arguments and calls main function """ # Parse arguments parser = getArgParser() args = parser.parse_args() args_dict = parseCommonArgs(args) # Create convert_args convert_keys = ['simple'] args_dict['convert_args'] = dict((k, args_dict[k]) for k in args_dict \ if k in convert_keys) for k in args_dict['convert_args']: del args_dict[k] # Calls header conversion function del args_dict['seq_files'] for f in args.__dict__['seq_files']: args_dict['seq_file'] = f convertHeaders(**args_dict)
default=default_usearch_exec, help='''The path to the usearch executable file.''') parser_ref.set_defaults(assemble_func=referenceAssembly) return parser if __name__ == '__main__': """ Parses command line arguments and calls main function """ # Parse arguments parser = getArgParser() args = parser.parse_args() args_dict = parseCommonArgs(args, in_arg='ref_file') # Convert case of fields if args_dict['head_fields']: args_dict['head_fields'] = list(map(str.upper, args_dict['head_fields'])) if args_dict['tail_fields']: args_dict['tail_fields'] = list(map(str.upper, args_dict['tail_fields'])) # Define assemble_args dictionary to pass to maskPrimers if args_dict['assemble_func'] is alignAssembly: args_dict['assemble_args'] = {'alpha': args_dict['alpha'], 'max_error': args_dict['max_error'], 'min_len': args_dict['min_len'], 'max_len': args_dict['max_len'], 'scan_reverse': args_dict['scan_reverse'], 'assembly_stats': AssemblyStats(args_dict['max_len'] + 1)} del args_dict['alpha'] del args_dict['max_error']
failed=False, log=False)], formatter_class=CommonHelpFormatter) parser.add_argument('--version', action='version', version='%(prog)s:' + ' %s-%s' %(__version__, __date__)) parser.add_argument('-l', nargs='+', action='store', dest='record_files', required=True, help='List of log files to parse.') parser.add_argument('-f', nargs='+', action='store', dest='fields', required=True, help='''List of fields to collect. The sequence identifier may be specified using the hidden field name "ID".''') return parser if __name__ == '__main__': """ Parses command line arguments and calls main function """ # Parse arguments parser = getArgParser() args = parser.parse_args() args_dict = parseCommonArgs(args, in_arg='record_files') # Convert case of fields if args_dict['fields']: args_dict['fields'] = list(map(str.upper, args_dict['fields'])) # Call parseLog for each log file del args_dict['record_files'] for f in args.__dict__['record_files']: args_dict['record_file'] = f tableLog(**args_dict)
'Assemble pairs by first attempting de novo assembly, then reference guided assembly.' ) parser_two.set_defaults(assemble_func=sequentialAssembly) return parser if __name__ == '__main__': """ Parses command line arguments and calls main function """ # Parse arguments parser = getArgParser() checkArgs(parser) args = parser.parse_args() args_dict = parseCommonArgs(args, in_arg='ref_file') # Convert case of fields if args_dict['head_fields']: args_dict['head_fields'] = list( map(str.upper, args_dict['head_fields'])) if args_dict['tail_fields']: args_dict['tail_fields'] = list( map(str.upper, args_dict['tail_fields'])) # Define assemble_args dictionary for join mode if args_dict['assemble_func'] is joinAssembly: args_dict['assemble_args'] = {'gap': args_dict['gap']} del args_dict['gap'] # Define assemble_args dictionary for align mode