paulirish / dna2json

Formats your genome file as JSON

Information

Package	dna2json
Description	Formats your DNA file as JSON
Node Version	>= 0.4

Terminology

SNP

A SNP (single-nucleotide polymorphism - pronounced "snip") is a mutation in your genome. SNPs can tell you a lot about yourself (hair color, height, muscle type, allergies, response to disease, response to pharmaceuticals, heritage, etc.).

Your DNA file from any vendor will be a big list of these SNPs. Think of it like a diff against a reference human genome. Most vendors will compare your genome against GRCh Build 37

Vendors

Name	Supported	Price	Sample	Autosomal SNPs	Y SNPs	X SNPs	MT SNPs	Raw Data
23andMe	Yes	99 USD	Saliva	967,000	3,089	26,087	2,737	Yes
ancestryDNA	Yes	99 USD	Saliva	682,549	885	17,604	0	Yes
FamilyTree	Yes	99 USD	Cheek Swab	708,092	0	18,091	0	Yes

tl;dr use 23andMe they provide more data and are the cheapest

CLI Usage

Use this if you just want to convert your data to the correct format so you can start querying your genome.

$ npm install dna2json -g
$ dna2json
Usage: dna2json <input file> <output file>
$ dna2json dna.txt dna.json
This will take a while...

It will stream the SNPs to disk as JSON - pretty easy.

Module Usage

var dna = require('dna2json');
var JSONStream = require('JSONStream');
var fs = require('fs');

// dna.createParser() returns a duplex stream
// input = text from your dna file
// output = SNPs as JSON
// to write to disk just pipe it to JSONStream then to fs

fs.createReadStream("dna.txt")
  .pipe(dna.createParser())
  .pipe(JSONStream.stringify())
  .pipe(fs.createWriteStream("dna.json"));

SNP-JSON

Every vendor has their own format for your DNA. I decided to make a standard format called SNP-JSON. This library will convert custom formats to this standard.

SNP-JSON looks like this

[
{"id":"rs10749813","c":1,"pos":73557945,"g":null},
{"id":"rs4128552","c":1,"pos":73560811,"g":"GT"},
{"id":"rs12033354","c":1,"pos":73573941,"g":"AG"},
{"id":"rs4603080","c":1,"pos":73579237,"g":"AG"},
{"id":"rs4582739","c":1,"pos":73602381,"g":"CT"},
{"id":"rs4452995","c":1,"pos":73613560,"g":"CT"}
]

Explanation:

Key	Description
id	RSID or vendor ID
c	Chromosome (1-22, X, Y, or MT)
pos	GRCh position
g	Genotype

Using your SNP-JSON

Once you have your data in the right format you can use the library of genosets by genomejs.

You can view a list of these at this npm search

You can also make your own tools that analyze your DNA however you want. It's yours! Here is a tool that will help query your DNA GQL

LICENSE

(MIT License)

Copyright (c) 2013 Fractal [email protected]

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.