pairToEvents: Read "pair" format of EMBOSS needle into GRanges as events.

In valenlab/amplican: Automated analysis of CRISPR experiments

Read "pair" format of EMBOSS needle into GRanges as events.

Description

Parse EMBOSS needle (or needleall) "pair" format into GRanges representation with events of deletions, insertions and mismatches. Make sure that each file corresponds to single subject (single amplicon). Assumes that bottom sequence "-bsequence" corresponds to the "subject" and full sequence alignment is returned.

Usage

pairToEvents(file, ID = "NA", strand_info = "+")

Arguments

file	(character) File path.
ID	(character) ID of the experiment, will be used as seqnames of the reutner ranges.
strand_info	(character) Strand to assign.

Value

(GRanges) Same as events.

valenlab/amplican documentation built on Jan. 28, 2024, 5:10 a.m.