Clustal example

index.js

// load the module
var Clustal = require("biojs-io-clustal");

// console
var current = document.createElement('p');
document.body.appendChild(current);

Clustal.read("http://dev.biojs-msa.org/v1/dummy/samples/p53.clustalo.clustal", function(seqs){
	current.innerHTML = seqs.length + " seqs have been loaded";
})

minified.js

require=function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);throw new Error("Cannot find module '"+o+"'")}var f=n[o]={exports:{}};t[o][0].call(f.exports,function(e){var n=t[o][1][e];return s(n?n:e)},f,f.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s}({c0FT7R:[function(require,module,exports){var Clustal,GenericReader,Seq,Str,__hasProp={}.hasOwnProperty,__extends=function(child,parent){for(var key in parent){if(__hasProp.call(parent,key))child[key]=parent[key]}function ctor(){this.constructor=child}ctor.prototype=parent.prototype;child.prototype=new ctor;child.__super__=parent.prototype;return child};Str=require("./strings");GenericReader=require("./generic_reader");Seq=require("./seq");module.exports=Clustal=function(_super){__extends(Clustal,_super);function Clustal(){return Clustal.__super__.constructor.apply(this,arguments)}Clustal.parse=function(text){var blockstate,k,label,line,lines,match,regex,seqCounter,seqs,sequence;seqs=[];lines=text.split("\n");if(lines[0].slice(0,6)===!"CLUSTAL"){throw new Error("Invalid CLUSTAL Header")}k=0;blockstate=1;seqCounter=0;while(k<lines.length){k++;line=lines[k];if(line==null||line.length===0){blockstate=1;continue}if(line.trim().length===0){blockstate=1;continue}else{if(Str.contains(line,"*")){continue}if(blockstate===1){seqCounter=0;blockstate=0}regex=/^(?:\s*)(\S+)(?:\s+)(\S+)(?:\s*)(\d*)(?:\s*|$)/g;match=regex.exec(line);if(match!=null){label=match[1];sequence=match[2];if(seqCounter>=seqs.length){seqs.push(new Seq(sequence,label,seqCounter))}else{seqs[seqCounter].seq+=sequence}seqCounter++}else{console.log(line)}}}return seqs};return Clustal}(GenericReader)},{"./generic_reader":3,"./seq":4,"./strings":5}],"biojs-io-clustal":[function(require,module,exports){module.exports=require("c0FT7R")},{}],3:[function(require,module,exports){var GenericReader,xhr;xhr=require("nets");module.exports=GenericReader=function(){function GenericReader(){}GenericReader.read=function(url,callback){var onret;onret=function(_this){return function(err,response,text){return _this._onRetrieval(text,callback)}}(this);return xhr(url,onret)};GenericReader._onRetrieval=function(text,callback){var rText;rText=this.parse(text);return callback(rText)};return GenericReader}()},{nets:6}],4:[function(require,module,exports){var Seq;module.exports=Seq=function(){function Seq(seq,name,id){var meta;this.seq=seq;this.name=name;this.id=id;meta={}}return Seq}()},{}],5:[function(require,module,exports){var strings;strings={contains:function(text,search){return"".indexOf.call(text,search,0)!==-1}};module.exports=strings},{}],6:[function(require,module,exports){var req=require("request");module.exports=Nets;function Nets(uri,opts,cb){req(uri,opts,cb)}},{request:7}],7:[function(require,module,exports){var window=require("global/window");var once=require("once");var messages={0:"Internal XMLHttpRequest Error",4:"4xx Client Error",5:"5xx Server Error"};var XHR=window.XMLHttpRequest||noop;var XDR="withCredentials"in new XHR?XHR:window.XDomainRequest;module.exports=createXHR;function createXHR(options,callback){if(typeof options==="string"){options={uri:options}}options=options||{};callback=once(callback);var xhr=options.xhr||null;if(!xhr){if(options.cors||options.useXDR){xhr=new XDR}else{xhr=new XHR}}var uri=xhr.url=options.uri||options.url;var method=xhr.method=options.method||"GET";var body=options.body||options.data;var headers=xhr.headers=options.headers||{};var sync=!!options.sync;var isJson=false;var key;if("json"in options){isJson=true;headers["Accept"]="application/json";if(method!=="GET"&&method!=="HEAD"){headers["Content-Type"]="application/json";body=JSON.stringify(options.json)}}xhr.onreadystatechange=readystatechange;xhr.onload=load;xhr.onerror=error;xhr.onprogress=function(){};xhr.ontimeout=noop;xhr.open(method,uri,!sync);if(options.withCredentials||options.cors&&options.withCredentials!==false){xhr.withCredentials=true}if(!sync){xhr.timeout="timeout"in options?options.timeout:5e3}if(xhr.setRequestHeader){for(key in headers){if(headers.hasOwnProperty(key)){xhr.setRequestHeader(key,headers[key])}}}else if(options.headers){throw new Error("Headers cannot be set on an XDomainRequest object")}if("responseType"in options){xhr.responseType=options.responseType}if("beforeSend"in options&&typeof options.beforeSend==="function"){options.beforeSend(xhr)}xhr.send(body);return xhr;function readystatechange(){if(xhr.readyState===4){load()}}function load(){var error=null;var status=xhr.statusCode=xhr.status;var body=null;if(xhr.response){body=xhr.body=xhr.response}else if(xhr.responseType==="text"||!xhr.responseType){body=xhr.body=xhr.responseText||xhr.responseXML}if(status===1223){status=204}if(status===0||status>=400&&status<600){var message=(typeof body==="string"?body:false)||messages[String(status).charAt(0)];error=new Error(message);error.statusCode=status}xhr.status=xhr.statusCode=status;if(isJson){try{body=xhr.body=JSON.parse(body)}catch(e){}}callback(error,xhr,body)}function error(evt){callback(evt,xhr)}}function noop(){}},{"global/window":8,once:9}],8:[function(require,module,exports){(function(global){if(typeof window!=="undefined"){module.exports=window}else if(typeof global!=="undefined"){module.exports=global}else{module.exports={}}}).call(this,typeof self!=="undefined"?self:typeof window!=="undefined"?window:{})},{}],9:[function(require,module,exports){module.exports=once;once.proto=once(function(){Object.defineProperty(Function.prototype,"once",{value:function(){return once(this)},configurable:true})});function once(fn){var called=false;return function(){if(called)return;called=true;return fn.apply(this,arguments)}}},{}]},{},[]);var Clustal=require("biojs-io-clustal");var current=document.createElement("p");document.body.appendChild(current);Clustal.read("http://dev.biojs-msa.org/v1/dummy/samples/p53.clustalo.clustal",function(seqs){current.innerHTML=seqs.length+" seqs have been loaded"});

package.json

{
  "name": "requirebin-sketch",
  "version": "1.0.0",
  "dependencies": {
    "biojs-io-clustal": "0.0.6"
  }
}

page-head.html

<style type='text/css'>html, body { margin: 0; padding: 0; border: 0; }
body, html { height: 100%; width: 100%; }</style>