config module¶
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class
mavis.config.
CustomHelpFormatter
(prog, indent_increment=2, max_help_position=24, width=None)[source]¶ Bases:
argparse.ArgumentDefaultsHelpFormatter
subclass the default help formatter to stop default printing for required arguments
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class
mavis.config.
LibraryConfig
(library, protocol, disease_status, bam_file=None, inputs=None, read_length=None, median_fragment_size=None, stdev_fragment_size=None, strand_specific=False, strand_determining_read=2, **kwargs)[source]¶ Bases:
mavis.constants.MavisNamespace
holds library specific configuration information
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class
mavis.config.
RangeAppendAction
(nmin=1, nmax=None, **kwargs)[source]¶ Bases:
argparse.Action
allows an argument to accept a range of arguments
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mavis.config.
augment_parser
(arguments, parser, required=None)[source]¶ Adds options to the argument parser. Separate function to facilitate the pipeline steps all having a similar look/feel
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mavis.config.
generate_config
(args, parser, log=<mavis.util.Log object>)[source]¶ Parameters: - parser (argparse.ArgumentParser) – the main parser
- required – the argparse required arguments group
- optional – the argparse optional arguments group
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mavis.config.
get_metavar
(arg_type)[source]¶ For a given argument type, returns the string to be used for the metavar argument in add_argument
Example
>>> get_metavar(bool) '{True,False}'
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mavis.config.
nameable_string
(input_string)[source]¶ A string that can be used for library and/or filenames
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mavis.config.
validate_section
(section, namespace, use_defaults=False)[source]¶ given a dictionary of values, returns a new dict with the values casted to their appropriate type or set to a default if the value was not given
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mavis.config.
write_config
(filename, include_defaults=False, libraries=[], conversions={}, log=<mavis.util.Log object>)[source]¶ Parameters: - filename (str) – path to the output file
- include_defaults (bool) – True if default parameters should be written to the config, False otherwise
- libraries (list of LibraryConfig) – library configuration sections
- conversions (dict of list by str) – conversion commands by alias name
- log (function) – function to pass output logging to