Package | gql |
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(snp, cb){
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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