Module spliceai

Write to a custom format useful for SpliceAi splice predictions

SpliceAI requires a gene annotation file. The file format is very similar to GenePred, but has only one record per gene and is thus not directly compatible with GenePred. Even though it is possible to run SpliceAI when the annotation file is grouped by transcripts, this Writer contains functionality to provide a gene-based annotation file.

The annotation file is created by merging all transcripts of a gene into a single transcript. The merging considers all exons of all transcripts. See merge for details how exons are merged.

Transcript 1   ----XXXXXX----XXXX------------XXXXXX---XXXX
Transcript 2   ----XXXXXX------------XXXX----XXXXXX---XXXX
Transcript 3   -------XXX------------------XXXXX------XXXX
Merged         ----OOOOOO----OOOO----OOOO--OOOOOOOO---OOOO

Structs

Writer

Writes Transcripts into a BufWriter to be used as gene annotation by SpliceAI