bioinformatics-parser/lib/fastq.js

.fasta and .fastq parsers

"use strict";

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

/*
 * fastq.js
 */
function parse(text) {
  var lines = text.trim().split('\n');
  if (lines.length % 4 !== 0) return failWith("line length isn't a multiple of 4: ".concat(lines.length));
  var entries = [];

  for (var i = 0; i < lines.length; i += 4) {
    var identifier = lines[i + 0];
    var sequence = lines[i + 1];
    var identifierPlus = lines[i + 2];
    var quality = lines[i + 3];
    if (!identifier.startsWith('@')) return failWith("identifier line doesn't start with @ (line ".concat(i + 1, ")"));else identifier = identifier.slice(1);
    if (!isAllowed(sequence)) return failWith("sequence line contains invalide characters (line ".concat(i + 1, ")"));
    if (!identifierPlus.startsWith('+')) return failWith("identifierPlus line doesn't start with @ (line ".concat(i + 1, ")"));else identifierPlus = identifierPlus.slice(1);
    if (quality.length !== sequence.length) return failWith("quality line length doesn't match sequence line length (line ".concat(i + 1, ")"));
    entries.push({
      identifier: identifier,
      sequence: sequence,
      identifierPlus: identifierPlus,
      quality: quality
    });
  }

  return {
    ok: true,
    error: undefined,
    result: entries
  };
}

function failWith(message) {
  return {
    ok: false,
    error: new Error('Invalid fastq file: ' + message),
    result: undefined
  };
}

function isAllowed(text) {
  for (var i = 0; i < text.length; i++) {
    if (!isAllowedCode(text.charCodeAt(i))) return false;
  }

  return true;
}

function isAllowedOrEmpty(text) {
  if (text.length === 0) return true;
  return isAllowed(text);
}

function isAllowedCode(code) {
  // FIXME: is it only ATCG ofr fastq?
  if (code >= 65
  /* A */
  && code <= 78
  /* N */
  || code >= 80
  /* P */
  && code <= 90
  /* Z */
  || code >= 97
  /* a */
  && code <= 110
  /* n */
  || code >= 112
  /* p */
  && code <= 122
  /* z */
  || code === 42
  /* * */
  || code === 45
  /* - */
  ) return true;
  return false;
}
/*
   Fasta format allowed chars:

        A  adenosine          C  cytidine             G  guanine
        T  thymidine          N  A/G/C/T (any)        U  uridine
        K  G/T (keto)         S  G/C (strong)         Y  T/C (pyrimidine)
        M  A/C (amino)        W  A/T (weak)           R  G/A (purine)
        B  G/T/C              D  G/A/T                H  A/C/T
        V  G/C/A              -  gap of indeterminate length

  For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are:

        A  alanine               P  proline
        B  aspartate/asparagine  Q  glutamine
        C  cystine               R  arginine
        D  aspartate             S  serine
        E  glutamate             T  threonine
        F  phenylalanine         U  selenocysteine
        G  glycine               V  valine
        H  histidine             W  tryptophan
        I  isoleucine            Y  tyrosine
        K  lysine                Z  glutamate/glutamine
        L  leucine               X  any
        M  methionine            *  translation stop
        N  asparagine            -  gap of indeterminate length
*/