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 it will return all properties and records.

For accessing all the records you can use GenomeDiff.parse('<string>').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:

let doc = GenomeDiff.parse('<string>'); // 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(<attribute>) method available on the record to do so:

let doc = GenomeDiff.parse('<string>'); // 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:

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.

Info

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This library adds an additional mutational type called MCDEL (it is not found in the bacterial genome reseq GD spec). This type is computed from a MC evidence type who's id is not referenced by any of the DEL mutations. This custom mutation type means that the MC evidence is interpreted as a DEL mutation.

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. 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:

"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"
]