constants module

mavis.annotate.constants.DEFAULTS = WeakMavisNamespace(_defns={'min_domain_mapping_match': 'a number between 0 and 1 representing the minimum percent match a domain must map to the fusion transcript to be displayed', 'min_orf_size': 'the minimum length (in amino acids) to retain a putative open reading frame (ORF)', 'max_orf_cap': 'the maximum number of ORFs to return (best putative ORFs will be retained)', 'annotation_filters': 'a comma separated list of filters to apply to putative annotations', 'draw_fusions_only': 'flag to indicate if events which do not produce a fusion transcript should produce illustrations', 'draw_non_synonymous_cdna_only': 'flag to indicate if events which are synonymous at the cdna level should produce illustrations'}, _types={'min_domain_mapping_match': <function float_fraction>, 'min_orf_size': <class 'int'>, 'max_orf_cap': <class 'int'>, 'annotation_filters': <class 'str'>, 'draw_fusions_only': <function cast_boolean>, 'draw_non_synonymous_cdna_only': <function cast_boolean>}, annotation_filters='choose_more_annotated,choose_transcripts_by_priority', draw_fusions_only=True, draw_non_synonymous_cdna_only=True, max_orf_cap=3, min_domain_mapping_match=0.9, min_orf_size=300)

• annotation_filters
• max_orf_cap
• min_domain_mapping_match
• min_orf_size

mavis.annotate.constants.SPLICE_SITE_RADIUS = 2

int – number of bases away from an exon boundary considered to be part of the splice site such that if it were altered the splice site would be considered to be abrogated.

mavis.annotate.constants.SPLICE_TYPE = MavisNamespace(COMPLEX='complex', MULTI_RETAIN='retained multiple introns', MULTI_SKIP='skipped multiple exons', NORMAL='normal', RETAIN='retained intron', SKIP='skipped exon', _defns={}, _types={'RETAIN': <class 'str'>, 'SKIP': <class 'str'>, 'NORMAL': <class 'str'>, 'MULTI_RETAIN': <class 'str'>, 'MULTI_SKIP': <class 'str'>, 'COMPLEX': <class 'str'>})

MavisNamespace – holds controlled vocabulary for allowed splice type classification values

• RETAIN: an intron was retained
• SKIP: an exon was skipped
• NORMAL: no exons were skipped and no introns were retained. the normal/expected splicing pattern was followed
• MULTI_RETAIN: multiple introns were retained
• MULTI_SKIP: multiple exons were skipped
• COMPLEX: some combination of exon skipping and intron retention