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 a person is sickle cell effected.

var gql = require('gql');
var dna = require('./genome.json');
 
var query = gql.or([
  gql.exact('rs334', 'TT'),
  gql.exact('i3003137', 'AA')
]);
 
var isMatch = query(dna);
console.log(isMatch); // true or false 

All of these APIs return a boolean-returning function that acts as the truth test. These functions take in one argument, a DNA-JSON object. You can nest as deep as you want, or be as basic as you want.

For example, checking if a person is immune to norovirus is pretty simple:

var dna = require('./my-dna.json');
 
var query = gql.exact('rs601338', 'AA');
var isImmune = query(dna);

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');

Inverts the result of another condition.

// evaluates to true if rs2032651 != AA 
var query = q.not(q.exact('rs2032651', 'AA'));
 
query({
  rs2032651: {
    genotype: 'TT'
  }
}); // true 
 
query({
  rs2032651: {
    genotype: 'AA'
  }
}); // false 

Evaluates to true if only the allele was observed at the specified position.

q.only('rs2032651', 'A'); // will match A, AA, AAA, etc. 

Evaluates to true if any of the given condition functions evaluate to true.

q.or([
  q.has('rs2032651', 'A'),
  q.doesntExist('rs2032651')
]);

Evaluates to true if all of the given condition functions evaluate to true.

q.and([
  q.exists('rs2032652'),
  q.has('rs2032651', 'A')
]);

Evaluates to true if all of the given condition functions evaluate to false.

q.none([
  q.has('rs2032651', 'A'),
  q.doesntExist('rs2032651')
]);

(MIT License)

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