https://github.com/biosustain/genomediff-node
GenomeDiff (*.gd) file parser for Node.js
https://github.com/biosustain/genomediff-node
breseq genomediff genomics parser
Last synced: 2 months ago
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GenomeDiff (*.gd) file parser for Node.js
- Host: GitHub
- URL: https://github.com/biosustain/genomediff-node
- Owner: biosustain
- License: mit
- Created: 2015-11-30T14:29:32.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2016-02-17T12:19:29.000Z (over 10 years ago)
- Last Synced: 2025-12-07T09:12:17.718Z (7 months ago)
- Topics: breseq, genomediff, genomics, parser
- Language: TypeScript
- Homepage:
- Size: 30.3 KB
- Stars: 2
- Watchers: 8
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Genomediff
> Parses strings from files in the GenomeDiff format generated by the breseq variant caller for haploid microbial organisms.
### Installation
----------------
```shell
$(node bin)/npm install genomediff
```
**Note**: It has only been tested with Node 5.
### Usage
---------
**GenomeDiff** strings are parsed using `GenomeDiff.parse()`. The **GenomeDiff** object contains a `metadata` dict with the meta data, as well as `mutations`, `evidence` and `validation` lists, each containing records of that type. Records can be accessed through this list or by id using `GenomeDiff.parse()[]`. **GenomeDiff** is an iterable and iterating it will return all properties and records.
For accessing all the records you can use `GenomeDiff.parse('').values()` which returns an iterable but only with the `Record` types.
For accessing the parents of a specific mutation you can use the `parents` property available on each record:
```js
let doc = GenomeDiff.parse(''); // a genomediff string
let someMutation = doc[12]; // mutation with id '12'
someMutation.parents // this will lookup all the parents of the record with id `12` and return as an array of Records
```
If you want to get an attribute from a parent record then you can use the `.get()` method available on the record to do so:
```js
let doc = GenomeDiff.parse(''); // a genomediff string
let someMutation = doc[12]; // mutation with id '12'
someMutation.get('coverage') // this will lookup all the parents of the record with id `12` and return the value of the attribute `coverage` if found on any of the parent records
```
If used with node, you can use the following:
```js
var GenomeDiff = require('genomediff').GenomeDiff;
var fs = require('fs');
var file = fs.readFileSync('', "utf8"); // path to your `.gd` file
var doc = GenomeDiff.parse(file);
```
If used in a browser, use:
```js
import {GenomeDiff} from 'genomediff';
var doc = GenomeDiff.parse(''); // a genomediff string
```
**Note**: Keep in mind that this package requires an ES6 environment in order to work.
### Running Tests
-----------------
A full test suite can be run using `npm test`. If you wish to run tests on file change, use `jasmine-node dist/ --autotest --color --verbose`.
### Development
---------------
When developing, use `tsc --watch` to build the `.ts` files on change. Alternatively, you can use `npm run build` if you do not wish to run the build on file change.
**Note**: If you add new files or remove files, make sure to edit the `"files"` field in `tsconfig.json`:
```js
"files": [
"./typings/typings.d.ts", // never remove this line
// add more files after this line
"./src/parser.ts",
"./src/parser.spec.ts",
"./src/records.ts",
"./src/records.spec.ts",
"./src/gd.ts",
"./src/gd.spec.ts"
]
```