biojs-io-fasta/lib/fasta.js

Parses FASTA files

// Generated by CoffeeScript 1.9.0
var Fasta, extend, st;

st = require("msa-seqtools");

extend = require("./extend");

module.exports = Fasta = {
  getMeta: st.getMeta,
  extend: function(metaParser) {
    var customFasta;
    customFasta = extend(Fasta);
    Fasta.getMeta = metaParser;
    return customFasta;
  },
  parse: function(text) {
    var currentSeq, getMeta, id, label, line, obj, seqs, _i, _len;
    seqs = [];
    if (!text || text.length === 0) {
      return [];
    }
    if (Object.prototype.toString.call(text) !== '[object Array]') {
      text = text.split("\n");
    }
    getMeta = Fasta.getMeta;
    for (_i = 0, _len = text.length; _i < _len; _i++) {
      line = text[_i];
      if (line[0] === ">" || line[0] === ";") {
        label = line.slice(1);
        obj = getMeta(label);
        label = obj.name;
        id = obj.id || seqs.length;
        currentSeq = new st.model("", obj.name, id);
        currentSeq.ids = obj.ids || {};
        currentSeq.details = obj.details || {};
        seqs.push(currentSeq);
      } else {
        currentSeq.seq += line;
      }
    }
    return seqs;
  },
  write: function(seqs, access) {
    var seq, text, _i, _len;
    text = "";
    for (_i = 0, _len = seqs.length; _i < _len; _i++) {
      seq = seqs[_i];
      if (access != null) {
        seq = access(seq);
      }
      text += ">" + seq.name + "\n";
      text += (st.splitNChars(seq.seq, 80)).join("\n");
      text += "\n";
    }
    return text;
  }
};