presto.Commandline
Commandline interface functions
- class presto.Commandline.CommonHelpFormatter(prog, indent_increment=2, max_help_position=24, width=None)
Bases:
RawDescriptionHelpFormatter
,ArgumentDefaultsHelpFormatter
Custom argparse.HelpFormatter
- presto.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
- presto.Commandline.getCommonArgParser(seq_in=True, seq_out=True, seq_paired=False, db_in=False, db_out=False, out_file=True, failed=True, log=True, annotation=True, multiproc=False, add_help=True)
Defines an ArgumentParser object with common pRESTO arguments
- Parameters:
seq_in (bool) – if True include sequence input arguments.
seq_out (bool) – if True include sequence output arguments.
seq_paired (bool) – if True defined paired-end sequence input and output arguments.
db_in (bool) – if True include tab-delimited database input arguments.
db_out (bool) – if True include tab-delimited database output arguments.
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.
annotation (bool) – If True include annotation arguments.
multiproc (bool) – If True include multiprocessing arguments.
add_help (bool) – If True add help and version arguments.
- Returns:
ArgumentParser object.
- Return type:
- presto.Commandline.parseCommonArgs(args, in_arg=None, in_types=None)
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’, ‘seq_files’, ‘seq_files_1’, ‘seq_files_2’, ‘primer_file’] 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
- Returns:
Dictionary copy of args with output arguments embedded in the dictionary out_args
- Return type: