g2p_mapper

A zero-dependency TypeScript library for mapping genome positions to protein/transcript positions and vice versa. Works with GFF3-style features and handles both forward and reverse strand genes, CDS phase offsets, and duplicate CDS deduplication.

Install

npm install g2p_mapper

Usage

Pass a transcript feature (with CDS subfeatures) to genomeToTranscriptSeqMapping:

import { genomeToTranscriptSeqMapping } from 'g2p_mapper'

const { g2p, p2g, refName, strand } = genomeToTranscriptSeqMapping(feature)

// g2p: Record<number, number> — maps genome position → protein position
// p2g: Record<number, number> — maps protein position → genome position

The input feature should match the Feat interface:

interface Feat {
  strand: number // 1 (forward) or -1 (reverse)
  refName: string // chromosome/contig name
  type: string // e.g. 'mRNA'
  phase: number // CDS phase (0, 1, or 2)
  id: string
  start: number // 0-based
  end: number // 0-based, half-open
  subfeatures?: Feat[] // should contain CDS children
}

Use getCodonRange to get the genomic coordinate range for a codon at a given protein position:

import { getCodonRange } from 'g2p_mapper'

// returns a 0-based half-open [start, end) interval, or undefined
const range = getCodonRange(p2g, proteinPos, strand)

See also

• https://github.com/cmdcolin/g2p_mapper_cli — CLI wrapper for this library
• https://github.com/cmdcolin/interproscan2genome — maps InterProScan protein annotations back to genome coordinates
• https://github.com/cmdcolin/jbrowse-plugin-protein3d - our plugin for mapping 3-D protein structure positions to the genome
• https://github.com/GMOD/jbrowse-plugin-msaview - our plugin for mapping MSA sequence positions to the genome

Publishing

Trusted publishing via GitHub Actions.

npm version patch  # or minor/major

Footnote

This package makes various assumptions about the biology, specifically simple 3-letter codon translation. This assumption may not be valid in all circumstances (biology breaks the rules constantly). Make sure to validate these assumptions for your application