presto.Commandline¶
Commandline interface functions
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class
presto.Commandline.
CommonHelpFormatter
(prog, indent_increment=2, max_help_position=24, width=None)¶ Bases:
argparse.RawDescriptionHelpFormatter
,argparse.ArgumentDefaultsHelpFormatter
Custom argparse.HelpFormatter
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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
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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:
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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: