mavis.annotate package

Submodules

• base module
• constants module
• file_io module
• genomic module
• main module
• protein module
• splicing module
• variant module

Module contents

Sub-package Documentation

Types of Output Files

expected name/suffix	file type/format	content
annotations.tab	text/tabbed	annotated events
annotations.fusion-cdna.fa	fasta	putative fusion unspliced cDNA sequences
drawings/*.svg	SVG	diagrams
drawings/*.legend.json	JSON	diagram legend/metadata

Algorithm Overview

see theory - annotating events

• read in breakpoint pairs
• generate strand-specific annotations (one annotation per strand, multiple if multiple genes/transcripts in the region)
• try building fusion transcripts for bp-specific calls
• generate SVG diagrams

Levels of Annotations

Overview of Class Relationships

The Annotation sub-package has objects for genetic annotations and related calculations. The basic layout of the package is shown above. IS-A relationships are given by the blue arrows. HAS-A relationships are shown in black. And reference_object/parent type relationships are shown in red. Gene is a gene. Start and end are genomic positions wrt to the template/chr. UsTranscript is the unspliced transcript. Start and end are genomic positions wrt to the template/chr. Transcript: is the spliced transcript. Start and end coordinates are 1 to the length of the spliced product in base pairs. Translation: is the translation of the spliced transcript. Start and end are cdna positions wrt the 5’ end of the spliced transcript. The start and end here describe the start and end of the coding sequence