alignment.js/helpers/fasta.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.fastaToText = fastaToText;
exports.fnaParser = fnaParser;
exports.fnaToText = fnaToText;
exports["default"] = void 0;

var _phylotree = require("phylotree");

var _jointSort = _interopRequireDefault(require("./jointSort.js"));

function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }

function _typeof(obj) { "@babel/helpers - typeof"; if (typeof Symbol === "function" && typeof Symbol.iterator === "symbol") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; } return _typeof(obj); }

function fastaParser(fasta) {
  if (_typeof(fasta) == "object") return fasta;
  var seqs = [],
      header,
      in_header,
      start,
      seq;

  for (var i = 0; i < fasta.length; i++) {
    if (fasta[i] == ">" || i == fasta.length - 1) {
      if (header) {
        seq = fasta.slice(start, i).replace(/\s/g, "");
        seqs.push({
          header: header,
          seq: seq
        });
      }

      in_header = true;
      start = i + 1;
    }

    if (fasta[i] == "\n" && in_header) {
      in_header = false;
      header = fasta.slice(start, i);
      start = i + 1;
    }
  }

  seqs.number_of_sequences = seqs.length;
  seqs.number_of_sites = seqs[0].seq.length;
  return seqs;
}

function fastaToText(fasta) {
  return fasta.map(function (entry) {
    return ">" + entry.header + "\n" + entry.seq;
  }).join("\n") + "\n";
}

function fnaParser(fna, sortFASTA) {
  var i = fna.length - 2,
      current_char = fna[i];

  while (current_char != "\n") {
    i--;
    current_char = fna[i];
  }

  var sequence_data = fastaParser(fna.slice(0, i + 1)),
      newick = fna.slice(i + 1, fna.length - 1),
      tree = new _phylotree.phylotree(newick);

  if (sortFASTA) {
    (0, _jointSort["default"])(sequence_data, tree);
  }

  return {
    sequence_data: sequence_data,
    tree: tree
  };
}

function fnaToText(fna) {
  return fna.sequence_data.map(function (record) {
    return ">" + record.header + "\n" + record.seq;
  }).join("\n") + "\n" + fna.tree.newick_string;
}

var _default = fastaParser;
exports["default"] = _default;