genoset-norovirus

Determines if a genome is immune to norovirus (rs601338)

npm install genoset-norovirus
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Information

Packagegenoset-norovirus
Description Determines if a genome is immune to norovirus (rs601338)
Node Version >= 0.4

Compatibility

This genoset is to be used with genomejs JSON. See the dna2json repository for more information.

Usage

This module simply exports a GQL query. Check out the GQL page for more information

This sample is just using the GQL streaming interface to figure out if a genome is a norovirus or not.

var norovirus = require('genoset-norovirus');
var fs = require('fs');
var path = require('path');
var es = require('event-stream');
var JSONStream = require('JSONStream');

var jsonStream = fs.createReadStream(path.join(__dirname, "dna.json"));

var query = norovirus();
var genoStream = query.stream();

jsonStream
  .pipe(JSONStream.parse('*'))
  .pipe(genoStream);

var count = 0;
genoStream.on('data', function(snp){
  console.log('Analyzed', ++count, 'SNPs');
});

genoStream.on('end', function(){
  console.log("There are", query.matches().length, "matches for norovirus immunity");
  console.log("There is a", query.percentage(), "percent chance that genoset matches");
});

LICENSE

(MIT License)

Copyright (c) 2013 Fractal contact@wearefractal.com

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.

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