config module¶
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class
mavis.config.
JobSchedulingConfig
(validate_memory_gb=12, default_memory_gb=10, queue='transabyss.q')[source]¶ Bases:
object
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class
mavis.config.
LibraryConfig
(library, protocol, disease_status, bam_file, inputs, read_length, median_fragment_size, stdev_fragment_size, stranded_bam, strand_determining_read=2, **kwargs)[source]¶ Bases:
object
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class
mavis.config.
PairingConfig
(split_call_distance=10, contig_call_distance=0, flanking_call_distance=0, spanning_call_distance=5, max_proximity=5000, low_memory=False)[source]¶ Bases:
object
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class
mavis.config.
ReferenceFilesConfig
(annotations=None, reference_genome=None, template_metadata=None, masking=None, aligner_reference=None, dgv_annotation=None, low_memory=False)[source]¶ Bases:
object
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class
mavis.config.
SummaryConfig
(filter_min_remapped_reads=5, filter_min_spanning_reads=5, filter_min_flanking_reads=5, filter_min_flanking_only_reads=10, filter_min_split_reads=5, filter_min_linking_split_reads=1, flanking_call_distance=0, split_call_distance=10, contig_call_distance=0, spanning_call_distance=5)[source]¶ Bases:
object
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mavis.config.
add_semi_optional_argument
(argname, success_parser, failure_parser, help_msg='')[source]¶ for an argument tries to get the argument default from the environment variable
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mavis.config.
get_env_variable
(arg, default, cast_type=None)[source]¶ Parameters: arg (str) – the argument/variable name Returns: the setting from the environment variable if given, otherwise the default value
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mavis.config.
read_config
(filepath)[source]¶ reads the configuration settings from the configuration file
Parameters: filepath (str) – path to the input configuration file Returns: list of Namespace
: namespace arguments for each libraryReturn type: class
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mavis.config.
write_config
(filename, include_defaults=False, libraries=[], conversions={}, log=<function devnull>)[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