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mavis.config

CONVERT_OPTIONS

CONVERT_OPTIONS = WeakMavisNamespace()

class mavis.config.CustomHelpFormatter

inherits argparse.ArgumentDefaultsHelpFormatter

subclass the default help formatter to stop default printing for required arguments

class mavis.config.RangeAppendAction

inherits argparse.Action

allows an argument to accept a range of arguments

mavis.config.RangeAppendAction.__init__()

def __init__(self, nmin=1, nmax=None, **kwargs):

Args

  • nmin
  • nmax

class mavis.config.LibraryConfig

inherits MavisNamespace

holds library specific configuration information

mavis.config.LibraryConfig.__init__()

def __init__(
    self,
    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
):

Args

  • library
  • protocol
  • disease_status
  • bam_file
  • inputs
  • read_length
  • median_fragment_size
  • stdev_fragment_size
  • strand_specific
  • strand_determining_read

mavis.config.LibraryConfig.build()

Builds a library config section and gathers the bam stats

@staticmethod
def build(
    library,
    protocol,
    bam_file,
    inputs,
    annotations=None,
    log=DEVNULL,
    distribution_fraction=0.98,
    sample_cap=3000,
    sample_bin_size=1000,
    sample_size=500,
    **kwargs
):

Args

  • library
  • protocol
  • bam_file
  • inputs
  • annotations
  • log
  • distribution_fraction
  • sample_cap
  • sample_bin_size
  • sample_size

class mavis.config.MavisConfig

inherits MavisNamespace

mavis.config.MavisConfig.read()

reads the configuration settings from the configuration file

@staticmethod
def read(filepath):

Args

  • filepath (str): path to the input configuration file

Returns

  • List[Namespace]: namespace arguments for each library

mavis.config.validate_section()

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

def validate_section(section, namespace, use_defaults=False):

Args

  • section
  • namespace
  • use_defaults

mavis.config.get_metavar()

For a given argument type, returns the string to be used for the metavar argument in add_argument

def get_metavar(arg_type):

Args

  • arg_type

Examples

>>> get_metavar(bool)
'{True,False}'

mavis.config.nameable_string()

A string that can be used for library and/or filenames

def nameable_string(input_string):

Args

  • input_string

mavis.config.augment_parser()

Adds options to the argument parser. Separate function to facilitate the pipeline steps all having a similar look/feel

def augment_parser(arguments, parser, required=None):

Args

  • arguments
  • parser
  • required