genomediff

Genomediff

Parses strings from files in the GenomeDiff format generated by the breseq variant caller for haploid microbial organisms.

Installation

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$(node bin)/npm install genomediff

Note: It has only been tested with Node 5.

Usage

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GenomeDiff strings are parsed using GenomeDiff.parse(<string>). 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(<string>)[<id>]. GenomeDiff is an iterable and iterating will return all records of all types.

For accessing the parents of a specific mutation you can use the .parents(<id>) method available on the document returned from GenomeDiff.parse(<string>):

let doc = GenomeDiff.parse('<string>'); // a genomediff string
doc.parents('<id>') // this will lookup all the parents of the record with `<id>`

If used with node, you can use the following:

var GenomeDiff = require('genomediff').GenomeDiff;
var fs = require('fs');
var file = fs.readFileSync('<path>', "utf8"); // path to your `.gd` file
var doc = GenomeDiff.parse(file);

If used in a browser, use:

import {GenomeDiff} from 'genomediff';
var doc = GenomeDiff.parse('<string>'); // a genomediff string

Note: Keep in mind that this package requires an ES6 environment in order to work.

Running Tests

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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

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When developing, use tsc --watch to build the .ts files on change.

Note: If you add new files or remove files, make sure to edit the "files" field in tsconfig.json:

"files": [
	"./tsd_typings/tsd.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"
]