msa-parsers

A TypeScript library for parsing multiple sequence alignment (MSA) files and related formats.

Part of react-msaview (JBrowseMSA).

Installation

npm install msa-parsers
# or
yarn add msa-parsers

Supported formats

MSA formats

• Stockholm - Stockholm format (used by Pfam, Rfam)
• FASTA - Aligned FASTA format
• Clustal - ClustalW/ClustalX format
• A3M - A3M format (used by HHsuite)
• EMF - Ensembl Multi Format

Other formats

• Newick - Phylogenetic tree format
• GFF - General Feature Format (with InterProScan conversion utilities)

Usage

Parsing MSA files

The parseMSA function auto-detects the format:

import { parseMSA } from 'msa-parsers'

const msa = parseMSA(fileContents)

// Get sequence names
const names = msa.getNames()

// Get a specific row
const sequence = msa.getRow('sequence_name')

// Get alignment width
const width = msa.getWidth()

// Get phylogenetic tree (if available)
const tree = msa.getTree()

Using specific parsers

import { FastaMSA, StockholmMSA, ClustalMSA } from 'msa-parsers'

const fasta = new FastaMSA(fastaContents)
const stockholm = new StockholmMSA(stockholmContents)
const clustal = new ClustalMSA(clustalContents)

Parsing Newick trees

import { parseNewick, generateNodeIds } from 'msa-parsers'

const tree = parseNewick('(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);')
const treeWithIds = generateNodeIds(tree)

GFF and InterProScan utilities

import { parseGFF, gffToInterProResults, interProToGFF } from 'msa-parsers'

// Parse GFF file
const records = parseGFF(gffContents)

// Convert between GFF and InterProScan formats
const interProResults = gffToInterProResults(records)
const gffString = interProToGFF(interProResults, seqId)

License

MIT