31 December 2010

Translating a DNA to a Protein using server-side javascript and C: my notebook

In my previous post , I used Node.js to translate a DNA to a protein on the Server-side, using javascript. In the following post, I again will translate a DNAn but this time by calling a specialized C program on the server side.

Source code


The C program

The C program reads a DNA string from stdin a translate it using the standard genetic code:
#include <stdio.h>
#include <ctype.h>
static const char* STD_GENETIC_CODE="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
static int base2index(int 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;
}
};
static char translate(int b1,int b2,int b3)
{
int base1= base2index(b1);
int base2= base2index(b2);
int base3= base2index(b3);
if(base1==-1 || base2==-1 || base3==-1)
{
return '?';
}
else
{
return STD_GENETIC_CODE[base1*16+base2*4+base3];
}
}
static int next_base(FILE* in)
{
int c;
while((c=fgetc(in))!=EOF)
{
if(isspace(c)) continue;
break;
}
return c;
}
int main(void)
{
while(!feof(stdin))
{
int b1=next_base(stdin);
if(b1==EOF) break;
int b2=next_base(stdin);
if(b2==EOF) break;
int b3=next_base(stdin);
if(b3==EOF) break;
fputc(
translate(b1,b2,b3),
stdout);
}
return 0;
}
view raw translate.c hosted with ❤ by GitHub

Compilation:
gcc -o /my/bin/path/translate translate.c

The Node.js script

When the Node.js server receive a DNA parameter, it spawns a new process to the C program and we write the DNA to this process via 'stdin'.
Each time a new 'data' event (containing the protein) is received, it is printed to the http response. At the end of the process, we close the stream by calling 'end()'.
/**
* Author:
* Pierre Lindenbaum
* Mail:
* plindenbaum@yahoo.fr
* WWW:
* http://plindenbaum.blogspot.com
* Motivation:
* Node.js script . translate a DNA to a protein using an external C program
* Usage:
* ${nodejs.dir}/node translate.js
*/
var spawn = require('child_process').spawn
var sys = require('sys');
querystring = require('querystring');
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'});
var child = spawn('/path/to/bin/translate',[]);
child.stdin.write(params.query.dna);
child.stdout.on('data', function (data) {
res.write(data);
});
child.stderr.on('data', function (data) {
console.log("stderr:"+data);
});
child.on('exit', function (data)
{
res.end();
});
child.stdin.end();
return;
}
}
res.writeHead(200, {'Content-type': 'text/html'});
res.end(
'<html><body><form action="/" method=\"GET\">'+
'<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/');
view raw translate.js hosted with ❤ by GitHub

test

> node-v0.2.5/node translate.js
Server running at http://127.0.0.1:8080

> curl -s "http://localhost:8080/?dna=ATGATGATAGATAGATATAGTAGATATGATCGTCAGCCATACG"
MMIDRYSRYDRQPY


That's it,

Pierre

Publié par Pierre Lindenbaum at 3:05 PM 0 commentaires

Libellés : , , , , ,

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.
/**
* 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/');
view raw translate.js hosted with ❤ by GitHub

Running the server

> node-v0.2.5/node translate.js
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

Publié par Pierre Lindenbaum at 1:47 PM 1 commentaires

Libellés : , , , ,

14 December 2010

Looking for an expert ?

Yesterday, Andrew Su asked on Biostar: "Given a gene, what is the best automated method to identify the world experts? ".

Here is my solution:

  • First for a given gene name, we use NCBI-ESearch to find its Gene-Id in NCBI Gene
  • The Gene record is then downloaded as XML using NCBI-EFetch
  • XPATH is used to retrieve all the articles in pubmed about this gene and identified by the XML tags <PubMedId>
  • Each article is downloaded from pubmed. The element <Affiliation> is extracted from the record; sometimes this tag contains the the main contact's email. The authors are also extracted and we count the number of times each author was found. I tried to solve the problem of ambiguity for the names of the authors by looking at the name, surname and initials. If an author's name was contained in the e-mail, it was affected to him
  • At the end, all the authors are sorted in function of the number of times they were seen and the most prolific author is printed out.


Source code

/**
* Author: Pierre Lindenbaum PhD
* WWW: http://plindenbaum.blogspot.com
* Motivation:
* Given a gene, identify the world experts
* http://biostar.stackexchange.com/questions/4296
*/
import java.net.URLEncoder;
import java.text.Collator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Set;
import java.util.TreeSet;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamWriter;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
public class BioStar4296
{
private Logger LOG=Logger.getLogger(BioStar4296.class.getName());
private String organism="Homo Sapiens";
private DocumentBuilder docBuilder;
private XPath xpath;
private Collator collator;
static class Author
{
String suffix="";
String firstName="";
String lastName="";
String initials="";
Set<String> mails=new HashSet<String>();
Set<Integer> pmids=new TreeSet<Integer>();
int factor=1;
Set<String> affilitations=new HashSet<String>();
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result
+ ((firstName == null) ? 0 : firstName.hashCode());
result = prime * result
+ ((lastName == null) ? 0 : lastName.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Author other = (Author) obj;
if (firstName == null) {
if (other.firstName != null)
return false;
} else if (!firstName.equals(other.firstName))
return false;
if (lastName == null) {
if (other.lastName != null)
return false;
} else if (!lastName.equals(other.lastName))
return false;
return true;
}
@Override
public String toString() {
return firstName+" "+lastName+" lab:"+this.affilitations+" mails:"+this.mails;
}
void write(XMLStreamWriter w)
throws Exception
{
w.writeStartElement("Person");
w.writeCharacters("\n");
w.writeStartElement("firstName");
w.writeCharacters(firstName);
w.writeEndElement();
w.writeCharacters("\n");
w.writeStartElement("lastName");
w.writeCharacters(lastName);
w.writeEndElement();
w.writeCharacters("\n");
for(Integer s:pmids)
{
w.writeStartElement("pmid");
w.writeCharacters(String.valueOf(s));
w.writeEndElement();
w.writeCharacters("\n");
}
for(String s:mails)
{
w.writeStartElement("mail");
w.writeCharacters(s);
w.writeEndElement();
w.writeCharacters("\n");
}
for(String s:affilitations)
{
w.writeStartElement("affilitation");
w.writeCharacters(s);
w.writeEndElement();
w.writeCharacters("\n");
}
w.writeEndElement();
w.writeCharacters("\n");
}
}
private BioStar4296() throws Exception
{
LOG.setLevel(Level.OFF);
DocumentBuilderFactory f=DocumentBuilderFactory.newInstance();
f.setNamespaceAware(false);
f.setCoalescing(true);
f.setIgnoringComments(true);
f.setIgnoringElementContentWhitespace(true);
f.setValidating(false);
this.docBuilder=f.newDocumentBuilder();
XPathFactory factory=XPathFactory.newInstance();
this.xpath=factory.newXPath();
this.collator= Collator.getInstance(Locale.FRENCH);
this.collator.setStrength(Collator.PRIMARY);
}
private int search(XMLStreamWriter w,String geneName)
throws Exception
{
w.writeCharacters("\n");
w.writeStartElement("gene");
w.writeAttribute("name", geneName);
String url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term="+
URLEncoder.encode(geneName+"[PREF] \""+this.organism+"\"[ORGN]", "UTF-8");
LOG.info(url);
Document dom=this.docBuilder.parse(url);
NodeList list=(NodeList)this.xpath.evaluate(
"/eSearchResult/IdList/Id",
dom,XPathConstants.NODESET);
if(list.getLength()==0)
{
w.writeComment("Cannot find any entry for "+geneName);
w.writeEndElement();
return -1;
}
else if(list.getLength()!=1)
{
w.writeComment("Ambigous name "+geneName);
w.writeEndElement();
return -1;
}
String geneId= list.item(0).getTextContent();
LOG.info("GeneId:"+geneId);
w.writeAttribute("geneId", geneId);
url="http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id="+
geneId+
"&rettype=text&retmode=xml";
LOG.info(url);
dom=this.docBuilder.parse(url);
list=(NodeList)this.xpath.evaluate(
"//PubMedId",
dom,XPathConstants.NODESET);
if(list.getLength()==0)
{
w.writeComment("No pubmed for "+geneName);
w.writeEndElement();
return -1;
}
List<Author> authors=new ArrayList<Author>();
Set<Integer> pmidSet=new TreeSet<Integer>();
for(int articleIdx=0;articleIdx< list.getLength();++articleIdx)
{
String pmid= list.item(articleIdx).getTextContent();
LOG.info("PMID:"+pmid);
pmidSet.add(Integer.parseInt(pmid));
}
w.writeAttribute("count-pmids",String.valueOf(pmidSet.size()));
w.writeCharacters("\n");
for(Integer pmid: pmidSet)
{
LOG.info("PMID:"+pmid);
url="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id="+pmid+"&retmode=xml";
LOG.info("url:"+url);
dom=this.docBuilder.parse(url);
Node n=(Node)this.xpath.evaluate("//Affiliation", dom,XPathConstants.NODE);
if(n==null) continue;
String affiliation=n.getTextContent();
String adressFragments[]=affiliation.split("[ \t\\:\\<,\\>\\(\\)]");
LOG.info("affiliation:"+affiliation);
NodeList authorList=(NodeList)this.xpath.evaluate(
"//AuthorList/Author",
dom,XPathConstants.NODESET);
LOG.info("Authors:"+authorList.getLength());
if(authorList.getLength()==0) continue;
for(int j=0;j< authorList.getLength();++j)
{
boolean collective=false;
Author author=new Author();
for(Node c1=authorList.item(j).getFirstChild();c1!=null;c1=c1.getNextSibling())
{
if(c1.getNodeType()!=Node.ELEMENT_NODE) continue;
String tag=c1.getNodeName();
String content= c1.getTextContent();
if(tag.equals("LastName"))
{
author.lastName= content;
}
else if(tag.equals("FirstName") || tag.equals("ForeName"))
{
author.firstName= content;
}
else if(tag.equals("Initials"))
{
author.initials= content;
}
else if(tag.equals("CollectiveName"))
{
collective=true;
break;
}
else if(tag.equals("Suffix"))
{
author.suffix= content;
}
}
if(collective) continue;
LOG.info("Make New Author:"+author);
int k=0;
for(k=0;k< authors.size();++k)
{
Author p=authors.get(k);
if( !p.firstName.isEmpty() &&
this.collator.compare(p.firstName,author.firstName)==0 &&
this.collator.compare(p.lastName,author.lastName)==0)
{
LOG.info("Same: "+p+" "+author);
author=p;
break;
}
}
if(k==authors.size())
{
k=0;
for(k=0;k< authors.size();++k)
{
Author p=authors.get(k);
if(
(
(!author.initials.isEmpty() && p.firstName.toLowerCase().startsWith(author.initials.toLowerCase())) ||
(!p.initials.isEmpty() && author.firstName.toLowerCase().startsWith(p.initials) )||
this.collator.compare(p.initials,author.initials)==0 )&&
this.collator.compare(p.lastName,author.lastName)==0)
{
LOG.info("Same: "+p+" "+author);
if(p.firstName.length()< author.firstName.length())
{
p.firstName=author.firstName;
}
author=p;
break;
}
}
}
if(k==authors.size())
{
LOG.info("Adding: "+author);
authors.add(author);
}
author.factor*=j;
author.affilitations.add(affiliation);
author.pmids.add(pmid);
if(affiliation.indexOf('@')!=-1)
{
for(String mail: adressFragments)
{
mail.replaceAll("\\{\\}", "");
if(mail.endsWith(".")) mail= mail.substring(0,mail.length()-1);
int index=mail.indexOf('@');
if(index==-1) continue;
String mailPrefix=mail.substring(0,index).toLowerCase();
if(mailPrefix.contains(author.lastName.toLowerCase()) ||
collator.compare(mailPrefix, author.lastName)==0)
{
LOG.info("Adding: "+mail+" to "+author);
author.mails.add(mail.toLowerCase());
}
else if( author.firstName.length()>1 &&
(mailPrefix.contains( author.firstName.toLowerCase()) ||
collator.compare(mailPrefix, author.firstName)==0))
{
LOG.info("Adding: "+mail+" to "+author);
author.mails.add(mail.toLowerCase());
}
}
}
}
}
if(authors.isEmpty())
{
w.writeComment("No Author found");
w.writeEndElement();
return -1;
}
Collections.sort(authors,new Comparator<Author>()
{
@Override
public int compare(Author o1, Author o2)
{
int i= o2.pmids.size()-o1.pmids.size();
if(i!=0) return i;
i= o2.factor-o1.factor;//later is more interesting ? not sure...
return i;
}
});
authors.get(0).write(w);
w.writeEndElement();
return 0;
}
public static void main(String[] args)
{
try {
BioStar4296 app= new BioStar4296();
int optind=0;
while(optind<args.length)
{
if(args[optind].equals("-h"))
{
System.err.println("Pierre Lindenbaum");
System.err.println("Options:");
System.err.println(" -o <organism> ["+app.organism+"]");
System.err.println(" -v show logs");
return;
}
else if(args[optind].equals("-o"))
{
app.organism=args[++optind];
}
else if(args[optind].equals("-v"))
{
app.LOG.setLevel(Level.ALL);
}
else if(args[optind].equals("--"))
{
optind++;
break;
}
else if(args[optind].startsWith("-"))
{
System.err.println("Unnown option: "+args[optind]);
return;
}
else
{
break;
}
++optind;
}
if(optind==args.length)
{
System.err.println("Gene Name missing");
}
else
{
XMLOutputFactory xmlfactory= XMLOutputFactory.newInstance();
XMLStreamWriter w= xmlfactory.createXMLStreamWriter(System.out,"UTF-8");
w.writeStartDocument("UTF-8","1.0");
w.writeCharacters("\n");
w.writeStartElement("experts");
w.writeCharacters("\n");
while(optind < args.length)
{
app.search(w,args[optind]);
optind++;
w.writeCharacters("\n");
}
w.writeEndElement();
w.writeEndDocument();
w.flush();
}
} catch (Exception e)
{
e.printStackTrace();
}
}
}
view raw BioStar4296.java hosted with ❤ by GitHub

Compilation

javac BioStar4296.java

Test

java BioStar4296 ZC3H7B eif4G1 PRNP

<?xml version="1.0" encoding="UTF-8"?>
<experts>
<gene name="ZC3H7B" geneId="23264" count-pmids="13">
<Person>
<firstName>Sumio</firstName>
<lastName>Sugano</lastName>
<pmid>8125298</pmid>
<pmid>9373149</pmid>
<pmid>14702039</pmid>
<affilitation>International and Interdisciplinary Studies, The University of Tokyo, Japan.</affilitation>
<affilitation>Institute of Medical Science, University of Tokyo, Japan.</affilitation>
<affilitation>Helix Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan.</affilitation>
</Person>
</gene>
<gene name="eif4G1" geneId="1981" count-pmids="106">
<Person>
<firstName>Nahum</firstName>
<lastName>Sonenberg</lastName>
<pmid>7651417</pmid>
<pmid>7935836</pmid>
<pmid>8449919</pmid>
(...)
<affilitation>Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, H3G 1Y6, Quebec, Canada.</affilitation>
<affilitation>Department of Biochemistry, McGill University, Montreal, Quebec, Canada.</affilitation>
<affilitation>Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA.</affilitation>
(...)
</Person>
</gene>
<gene name="PRNP" geneId="5621" count-pmids="429">
<Person>
<firstName>John</firstName>
<lastName>Collinge</lastName>
<pmid>1352724</pmid>
<pmid>1677164</pmid>
<pmid>2159587</pmid>
<pmid>20583301</pmid>
(...)
<mail>j.collinge@ic.ac.uk</mail>
<affilitation>Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.</affilitation>
<affilitation>MRC Prion Unit and Department of Neurogenetics, Imperial College School of Medicine at St. Mary's, London, United Kingdom. J.Collinge@ic.ac.uk</affilitation>
<affilitation>Division of Neuroscience (Neurophysiology), Medical School, University of Birmingham, Edgbaston, Birmingham, UK. sratte@pitt.edu</affilitation>
(...)
</Person>
</gene>
</experts>

about this result


  • ZC3H7B the result is wrong. In Dr Sugano's article (3 articles) ZC3H7B was present in among a large set of other genes used in his studies. The expert would be Dr D. Poncet, my former thesis advisor but he 'only' wrote two articles about this protein.
  • Eif4G1: I know Dr Sonenberg is the expert. His email wasn't found.
  • PRNP Collinge seems to be the expert. Dr Collinge's e-mail was detected.


That's it,

Pierre

Publié par Pierre Lindenbaum at 9:47 PM 1 commentaires

Libellés : , , , , , ,

13 December 2010

A new journal: BMC Open Research Computation #OpenResComp


Citing ''Aims & scope'':Open Research Computation publishes peer reviewed articles that describe the development, capacities, and uses of software designed for use by researchers in any field.

Submissions relating to software for use in any area of research are welcome as are articles dealing with algorithms, useful code snippets, as well as large applications or web services, and libraries.

Open Research Computation differs from other journals with a software focus in its requirement for the software source code to be made available under an Open Source Initiative compliant license, and in its assessment of the quality of documentation and testing of the software.

In addition to articles describing software Open Research Computation also welcomes submissions that review or describe developments relating to software based tools for research. These include, but are not limited to, reviews or proposals for standards, discussion of best practice in research software development, educational and support resources and tools for researchers that develop or use software based tools.

See also the insights from Cameron Neylon, Jan Aerts, Neil 10K Saunders ...

Publié par Pierre Lindenbaum at 8:38 PM 3 commentaires

Libellés : , , , ,

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