changeo.Commandline
Commandline interface
- class changeo.Commandline.CommonHelpFormatter(prog, indent_increment=2, max_help_position=24, width=None)
Bases:
RawDescriptionHelpFormatter
,ArgumentDefaultsHelpFormatter
Custom argparse.HelpFormatter
- changeo.Commandline.checkArgs(parser)
Checks that arguments have been provided and prints help if they have not.
- Parameters:
parser – An argparse.ArgumentParser defining the commandline arguments.
- Returns:
True if arguments are present. Prints help and exits if not.
- Return type:
boolean
- changeo.Commandline.getCommonArgParser(db_in=True, db_out=True, out_file=True, failed=True, log=True, format=True, multiproc=False, add_help=True)
Defines an ArgumentParser object with common pRESTO arguments
- Parameters:
db_in (bool) – if True include tab delimited database input arguments.
db_out (bool) – if True include explicit output file name argument.
out_file (bool) – if True add explicit output file name arguments.
failed (bool) – if True include arguments for output of failed results.
log (bool) – if True include log arguments.
format (bool) – input and output type arguments.
multiproc (bool) – if True include multiprocessing arguments.
- Returns:
an argument parser.
- Return type:
- changeo.Commandline.parseCommonArgs(args, in_arg=None, in_types=None, in_list=False)
Checks common arguments from getCommonArgParser and transforms output options to a dictionary
- Parameters:
args – Argument Namespace defined by ArgumentParser.parse_args.
in_arg – String defining a non-standard input file argument to verify; by default ‘db_files’ and ‘seq_files’ are supported in that order.
in_types – List of types (file extensions as strings) to allow for files in file_arg; if None do not check type.
in_list – if True allow multiple input files with the out_name and log arguments.
- Returns:
Dictionary copy of args with output arguments embedded in the dictionary out_args
- Return type:
- changeo.Commandline.setDefaultFields(args, defaults, format='airr')
Sets default field arguments by format