https://github.com/bcgsc/pori_graphkb_parser

A package for parsing and recreating HGVS-like variant notation used in GraphKB
https://github.com/bcgsc/pori_graphkb_parser

genomics knowledge-base personalized-medicine pori variant-notation

Last synced: 7 days ago
JSON representation

A package for parsing and recreating HGVS-like variant notation used in GraphKB

• Host: GitHub
• URL: https://github.com/bcgsc/pori_graphkb_parser
• Owner: bcgsc
• License: gpl-3.0
• Created: 2020-12-17T19:23:10.000Z (almost 4 years ago)
• Default Branch: develop
• Last Pushed: 2023-08-03T14:43:53.000Z (over 1 year ago)
• Last Synced: 2024-10-28T22:17:28.235Z (18 days ago)
• Topics: genomics, knowledge-base, personalized-medicine, pori, variant-notation
• Language: TypeScript
• Homepage: https://bcgsc.github.io/pori
• Size: 1.43 MB
• Stars: 4
• Watchers: 6
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# GraphKB Parser

[![codecov](https://codecov.io/gh/bcgsc/pori_graphkb_parser/branch/master/graph/badge.svg?token=D3IG5YL6JT)](https://codecov.io/gh/bcgsc/pori_graphkb_parser) ![build](https://github.com/bcgsc/pori_graphkb_parser/workflows/build/badge.svg?branch=master) [![npm version](https://badge.fury.io/js/%40bcgsc-pori%2Fgraphkb-parser.svg)](https://badge.fury.io/js/%40bcgsc-pori%2Fgraphkb-parser) ![node versions](https://img.shields.io/badge/node-12%20%7C%2014%20%7C%2016-blue)

This repository is part of the [platform for oncogenomic reporting and interpretation](https://github.com/bcgsc/pori).

- [About](#about)

- [Getting Started](#getting-started)

## About

The GraphKB parser is a node module for parsing variant notation and producing strings from

parsed notation.

## Getting Started

Import the package (Or try it out online with [RunKit](https://runkit.com/creisle/6083062ff39ff0001b93ea6f))

```js

const {parseVariant, stringifyVariant, jsonifyVariant} = require('@bcgsc-pori/graphkb-parser');

```

To use the variant parser methods simply pass a string into

```js

> const parsedResult = parseVariant('FEATURE:p.G12D');

{

    'prefix': 'p',

    ...

}

```

Which returns a variant notation object. This can be turned back into a string

```js

> stringifyVariant(parsedResult);

'FEATURE:p.G12D'

```

or a JSON (removes extra attributes used by parse methods)

```js

> jsonifyVariant(parsedResult)

```

If the notation is improperly formatted, the parse function will raise a parsing error

```js

try {

   const parsedResult = parseVariant('FEATUREp.G12D');

} catch (err) {

    if (err instanceof kbp.error.ParsingError) {

        console.log('Error in parsing the notation');

    }

}

```

See [notation](doc/notation.md) for information regarding the notation syntax.