precisely / seqvarnomjs

Sequence Variant Nomenclature Parser

SEQVARNOMJS

Javascript parser for Sequence Variant Nomenclature.

Quick Start

Note: this is a private repo hosted on Github, so you need to:

yarn install [email protected]/precisely/seqvarnomjs

Example

var svn = require('seqvarnomjs');

var pattern = svn.parse('NC0001_1.11:g.111T>G');
var genotype = svn.parse('NC0001_1.11:g.[111T>G];[111=]');

svn.match(pattern, genotype); // => true

Details

This library interprets SVN strings such as:

• simple variants NC00001_1.11:g.111T>G
• wild type NC00001_1.11:g.111=
• compound cis variants NC0001_1.11:g.[111T>G;222A>G]
  • 111T>G and 222A>G are on the same chromosome copy
• trans variants NC0001_1.11:g.[111T>G];[222A>G]
  • 111T>G and 222A>G are on different chromosome copies
• variants with uncertain phasing NC0001_1.11:g.[111T>G](;)[222A>G]
  • 111T>G and 222A>G may be on same chromosome copy or different ones
• complex variants NC0001_1.11:g.[111T>G;222A>G];[333=](;)[444T>A];[555G>A]

E.g.,

• match a variant:

  const genotype = parse('NC0001_1.11:g.[111T>G]');
  const pattern = parse('NC0001_1.11:g.[111T>G]');
  genotype.matches(pattern); // => true

• match a part of a variant:

  const genotype = parse('NC0001_1.11:g.[111T>G;222=](;)[333G>C;111=]');
  const pattern = parse('NC0001_1.11:g.[111T>G]');
  genotype.matches(pattern); // => true