peptide-cutter/index.js

A library for digesting amino acid sequences using rules from Expasy

var expasy_rules = require('./expasy_rules.json');

module.exports = class PeptideCutter {
  constructor(options = {}) {
    // These are the default values. They will
    // be overwritten by anything passed in 
    // through the options
    this.enzyme = 'trypsin';
    this.num_missed_cleavages = 0;
    this.min_length = 8;
    this.max_length = 30;

    if(options.enzyme !== undefined) {
      this.enzyme = options.enzyme;
      if(expasy_rules[this.enzyme] === undefined) {
        console.log("Invalid enzyme. Defaulting to trypsin");
        this.enzyme = 'trypsin';
      }
    }
    this.regex = new RegExp(expasy_rules[this.enzyme], "g");

    if(options.num_missed_cleavages !== undefined) {
      this.num_missed_cleavages = options.num_missed_cleavages;
      if(this.num_missed_cleavages < 0) {
        console.log("The number of missed cleavages can't be less than 0. Defaulting to 0");
        this.num_missed_cleavages = 0;
      }
    }

    if(options.min_length !== undefined) {
      this.min_length = options.min_length;
    }
    if(options.max_length !== undefined) {
      this.max_length = options.max_length;
    }
    if(this.min_length > this.max_length) {
      console.log("The min_length cannot be greater than the max_length. Defaulting to 8 and 30");
      this.min_length = 8;
      this.max_length = 30;
    }
  }

  cleave(sequence) {
    sequence = sequence.toUpperCase();
    var peptides = [];
    var num_missed = this.num_missed_cleavages;

    // Gather the cleavage sites
    var indices = [0];
    var m;
    do {
      m = this.regex.exec(sequence);
      if (m) {
        indices.push(m.index + 1);
      }
    } while (m);
    indices.push(sequence.length);
    indices = Array.from(new Set(indices)); // To make sure we don't have any duplicates which can cause issues

    // If there are only 3 cleavage sites there
    // is no reason to allow more than 3 missed
    // cleavages
    if(indices.length < num_missed) {
      num_missed = indices.length;
    }

    let indexLength = indices.length;
    for(var i=0; i<indexLength; i++) {
      for(var j=i; j<indexLength; j++) {
        if(j-i-1 > num_missed) {
          break;
        }
        var start_index = indices[i];
        var end_index = indices[j];
        if(start_index === end_index) {
          continue;
        }
        if(end_index - start_index >= this.min_length && end_index - start_index <= this.max_length) {
          peptides.push({
            sequence: sequence.substring(start_index, end_index),
            start: start_index,
            end: end_index-1,
            missed: j-i-1
          });
        }
      }
    }

    return peptides;
  }

}