main module

mavis.annotate.main.get_exon_annotations(translation)

mavis.annotate.main.main(inputs, output, reference_genome, annotations, template_metadata, min_domain_mapping_match=0.9, min_orf_size=300, max_orf_cap=3, annotation_filters='choose_more_annotated, choose_transcripts_by_priority', **kwargs)

Parameters:

• inputs (List of str) – list of input files to read
• output (str) – path to the output directory
• reference_genome (object) – see load_reference_genome()
• annotations (object) – see load_reference_genes()
• template_metadata (object) – see load_templates()
• min_domain_mapping_match (float) – min mapping match percent (0-1) to count a domain as mapped
• min_orf_size (int) – minimum size of an open reading frame to keep as a putative translation
• max_orf_cap (int) – the maximum number of open reading frame s to collect for any given event