Server-side javascript: translating a DNA with Node.js
(wikipedia) Node.js is an evented I/O framework for the V8 JavaScript engine on Unix-like platforms. It is intended for writing scalable (javascript-based) network programs such as web servers.
In the following post I will create a javascript server translating a DNA to a protein.
Installing Node.js
I've downloaded the sources for Node.js from http://nodejs.org/#download. It compiled (configure+make) and ran without any problem.The script
The following script contains a class handling a GeneticCode and the server TranslateDna translating the DNA to a protein, it handles both the POST and the GET http methods. It no parameter is found it displays a simple HTML form, else the form data are decoded and the DNA is translated. The protein is returned as a JSON structure.
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| /** | |
| * Author: | |
| * Pierre Lindenbaum | |
| * Mail: | |
| * plindenbaum@yahoo.fr | |
| * WWW: | |
| * http://plindenbaum.blogspot.com | |
| * Motivation: | |
| * my first Node.js script . translate a DNA to a protein | |
| * Usage: | |
| * ${nodejs.dir}/node script.js | |
| */ | |
| var sys = require('sys'); | |
| querystring = require('querystring'); | |
| /** class GeneticCode */ | |
| function GeneticCode(name,ncbiString) | |
| { | |
| this.name=name; | |
| this.ncbiString=ncbiString; | |
| }; | |
| /** std genetic code */ | |
| GeneticCode.STANDARD=new GeneticCode( | |
| "standard", | |
| "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" | |
| ); | |
| GeneticCode.prototype.base2index=function(c) | |
| { | |
| switch(c) | |
| { | |
| case 'T':case 't': return 0; | |
| case 'C':case 'c': return 1; | |
| case 'A':case 'a': return 2; | |
| case 'G':case 'g': return 3; | |
| default: return -1; | |
| } | |
| }; | |
| GeneticCode.prototype.translate=function( b1, b2, b3) | |
| { | |
| if(arguments.length==1) | |
| { | |
| var prot=""; | |
| for(var i=0;i+2 < b1.length;i+=3) | |
| { | |
| prot+= this.translate(b1[i],b1[i+1],b1[i+2]); | |
| } | |
| return prot; | |
| } | |
| var base1= this.base2index(b1); | |
| var base2= this.base2index(b2); | |
| var base3= this.base2index(b3); | |
| if(base1==-1 || base2==-1 || base3==-1) | |
| { | |
| return '?'; | |
| } | |
| else | |
| { | |
| return this.ncbiString[base1*16+base2*4+base3]; | |
| } | |
| } | |
| function TranslateDna(req,res) | |
| { | |
| if(req.method == 'GET') | |
| { | |
| var params = require('url').parse(req.url,true); | |
| if(params && params.query && params.query.dna) | |
| { | |
| res.writeHead(200, {'Content-type': 'text/plain'}); | |
| res.write(JSON.stringify({'protein':GeneticCode.STANDARD.translate(params.query.dna.replace(/\s/g,"")),'query':params.query.dna})); | |
| res.end(); | |
| return; | |
| } | |
| } | |
| else if(req.method=='POST') | |
| { | |
| var query = ""; | |
| req.addListener('data', function (chunk) { | |
| query+=chunk; | |
| }); | |
| req.addListener('end', function (chunk) | |
| { | |
| var params = querystring.parse(query); | |
| if(params && params.dna) | |
| { | |
| res.writeHead(200, {'Content-type': 'text/plain'}); | |
| res.write(JSON.stringify({'protein':GeneticCode.STANDARD.translate(params.dna.replace(/\s/g,"")),'query': params.dna})); | |
| res.end(); | |
| return; | |
| } | |
| }); | |
| return; | |
| } | |
| res.writeHead(200, {'Content-type': 'text/html'}); | |
| res.end( | |
| '<html><body><form action="/" method=\"'+ | |
| (Math.random()<0.5?"GET":"POST") | |
| +'\">'+ | |
| '<h1>DNA</h1>'+ | |
| '<textarea name="dna"></textarea><br/>' + | |
| '<input type="submit" value="Submit">' + | |
| '</form></body></html>' | |
| ); | |
| } | |
| http = require('http'); | |
| var nodeserver = http.createServer(TranslateDna); | |
| nodeserver.listen(8080); | |
| console.log('Server running at http://127.0.0.1:8080/'); |
Running the server
> node-v0.2.5/node translate.js
Server running at http://127.0.0.1:8080
Server running at http://127.0.0.1:8080
Test
> curl "http://localhost:8080/"
<html><body><form action="/" method="GET"><h1>DNA</h1><textarea name="dna"></textarea><br/><input type="submit" value="Submit"></form></body></html>
> curl "http://localhost:8080/?dna=ATGAACTATCGATGCTACGACTGATCG"
{"protein":"MNYRCYD*S","query":"ATGAACTATCGATGCTACGACTGATCG"}
That's it,
Pierre
1 comment:
Hi
Can node.js be used to find bone marrow transplant donors from complete human genomes databases on AWS?
Or are we better off using
c/c++/java/python/ruby ?
Are there existing libraries ?
Thanks
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