alignment.js/helpers/nucleotideComposition.js

A suite of reusable [React](http://reactjs.org/) components for creating a variety of visualizations involving [multiple sequence alignments](https://en.wikipedia.org/wiki/Multiple_sequence_alignment). [View the live demo here](http://alignment.hyphy.org/

"use strict";

Object.defineProperty(exports, "__esModule", {
  value: true
});
exports.siteComposition = siteComposition;

function _createForOfIteratorHelper(o) { if (typeof Symbol === "undefined" || o[Symbol.iterator] == null) { if (Array.isArray(o) || (o = _unsupportedIterableToArray(o))) { var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var it, normalCompletion = true, didErr = false, err; return { s: function s() { it = o[Symbol.iterator](); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it["return"] != null) it["return"](); } finally { if (didErr) throw err; } } }; }

function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(n); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }

function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }

function siteComposition(alignmentData, callback) {
  // Takes alignmentData in the format that alignment.js uses (i.e. an array with of sequences each with {header: <header>, seq: "AGCT..."} )
  // Returns the percentage of each nucleotide in the form of: {A: [0, 0.75, 1, 0.2, etc], G: [0, 0.25, 0, 0.4, etc], etc}
  //TODO: check to ensure that all sequences are the same length and/or handle sequences of different lengths.
  var composition = {};
  var sequenceLength = alignmentData[0].seq.length;
  var numberOfSequences = alignmentData.length;

  var _iterator = _createForOfIteratorHelper(alignmentData),
      _step;

  try {
    for (_iterator.s(); !(_step = _iterator.n()).done;) {
      var sequenceObject = _step.value;
      var sequence = sequenceObject.seq;

      for (var siteNumber = 0; siteNumber < sequence.length; siteNumber++) {
        var _nucleotide = sequence[siteNumber];

        if (!(_nucleotide in composition)) {
          composition[_nucleotide] = Array(sequenceLength).fill(0);
        }

        composition[_nucleotide][siteNumber]++;
      }
    }
  } catch (err) {
    _iterator.e(err);
  } finally {
    _iterator.f();
  }

  for (var nucleotide in composition) {
    composition[nucleotide] = composition[nucleotide].map(function (count) {
      return count / numberOfSequences;
    });
  }

  if (callback) {
    callback(composition);
  } else {
    return composition;
  }
}