Parse mutations from (type, pos, alt) to amino acid

As with many things in this repo, lovingly stolen from the seq_utils.py script in https://github.com/PoonLab/gromstole (as well as PoonLab/covizu).

Usage

parse_mutation(
  type,
  pos,
  alt,
  reffile = system.file("extdata/NC_045512.fa", package = "provoc")
)

Arguments

type

Either "~", "+", or "-" for mutation, insertion, or deletion, respectively.

pos

The one-indexed position relative to the reference.

alt

The alternate nucleotide, nucleotides, or number of deletions, respectively.

reffile

The path to the reference file that was used to define mutations. Usually NC_045512.fa except in very particular circumstances.

Value

e.g. aa:orf1a:K856R