constants module

mavis.annotate.constants.DEFAULTS = WeakMavisNamespace(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

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.

Type:int

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')

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

Type:MavisNamespace