gql

Query language for interpreting genome SNPs

Packagegql
Description Query language for interpreting genome SNPs
Node Version >= 0.4

This query language is for use with the genomejs JSON format. See the dna2json repository for more information.

This example will create a query that determines if the gender is male.

var gql = require('gql');
 
var query = gql.query();
query.needs(2);
query.exact("rs2032651", "D");
query.has("rs2032651", "A");
query.has("rs9341296", "C");
query.has("rs9341296", "T");
query.has("rs13304168", "C");
query.has("rs13304168", "T");
query.has("rs1118473", "A");
query.has("rs1118473", "G");
query.has("rs150173", "A");
query.has("rs150173", "C");
query.has("rs16980426", "G");
query.has("rs16980426", "T");
query.or(query.exact("rs1558843", "C"), query.exact("rs1558843", "A"));
query.or(query.exact("rs17222419", "C"), query.exact("rs17222419", "T"));
var async = require('async');
var snps = require('./genome.json');
async.forEach(snps, query.process.bind(query), function(){
  console.log(query.matches().length, "matches for genoset 144");
  console.log(query.percentage(), "chance that gene matches");
});
var async = require('async');
var JSONStream = require('JSONStream');
var fs = require('fs');
 
var jsonStream = fs.createReadStream('./genome.json');
 
var queryStream = query.stream();
 
jsonStream
  .pipe(JSONStream.parse('*'))
  .pipe(queryStream);
 
queryStream.on('end', function(){
  console.log(query.matches().length, "matches for genoset 144");
  console.log(query.percentage(), "chance that gene matches");
});

Creates a new GQL chainable query. Keep in mind that each condition is tested against one SNP at a time. If the condition is met then it is marked as a match and not tested again.

Evaluates to true if this was the only allele observed

q.exact("rs2032651", "D"); // will only match genotype D 
q.exact("rs2032651", "AT"); // will only match genotype AT 

Evaluates to true if the allele was observed at all

q.has("rs2032651", "A"); // will match GA, GAT, AB, etc. 

Evaluates to true if any allele has been observed

q.exists("rs2032651");

Evaluates to true if no allele has been observed

q.doesntExist("rs2032651");

Evaluates to true if any of the argument conditions evaluates to true

q.or(q.has("rs2032651", "A"), q.doesntExist("rs2032651"));

Evaluates to true if all of the argument conditions evaluates to true

q.and(q.exists("rs2032651"), q.has("rs2032651", "A"));

This will let you add a custom condition. Callback signature is (error, isMatch)

q.add(function(snpcb){
  cb(null, (snp.id === "rswhatever" && snp.genotype === "A"))
});

Adjusts the reporting of percentages. For example, to determine if a genome is male I only need to two matches for it to be 100% (even though I have 12 possible SNPs). 4 matches should be 200% not 33% in this scenario.

q.exact("rs2032651", "D"); // will only match genotype D 
q.exact("rs2032651", "AT"); // will only match genotype AT 

Runs the SNP through all of the conditions. If a condition is evaluated as true it will not be evaluated again and a match for it will be registered.

Turns the query into a through stream. Sugar for es.map(q.process);

Returns expecting/matches

Returns condition matches so far

Returns all conditions yet to be matched

Returns true or false if all conditions have been matches

(MIT License)

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