How To Get A Dbsnp Data From Java?

Question

[burcakotlu]

Hi,

Is there a way to get chrName, chrPosition and observed alleles of a given dbSNP rsId in java program?

and

Is there a way to get observed alleles of a SNP given with chrName and chrPosition in java program?

Thanks, Burçak

[burcakotlu]

I have two questions: 1. question input dbSNP rsId output: chrName, chrPosition, observedAlleles 2. question input chrName, chrPosition output: observedAlleles, dnSNP rsId

I just edited the tags.

Answer 1

[Pierre Lindenbaum]

EDIT: You changed the original question

from

Is there a way to get chrName, chrPosition and observed alleles of a given dbSNP rsId in java program?

to

Is there a way to get observed alleles of a SNP given with chrName and chrPosition in java program?

=> This is not the same problem = I wasted my time.

---

use xjc to generate classes from the XML schema spec:

xjc "ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.3.xsd"

compile the following program: (it calls NCBI E-Efetch , parses the SNP structure and loop over the mapping components )

import gov.nih.nlm.ncbi.snp.docsum.*;

import java.util.ArrayList;
import java.io.InputStream;
import java.util.List;


import javax.xml.bind.*;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
import javax.xml.transform.stream.StreamSource;

public class Biostar95284
    {
    private Unmarshaller unmarshaller;
    private static gov.nih.nlm.ncbi.snp.docsum.ObjectFactory _fool_javac=null;
    private  XMLInputFactory xmlInputFactory=null;
    private Biostar95284() throws Exception
        {
        this.xmlInputFactory = XMLInputFactory.newInstance();
        xmlInputFactory.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, Boolean.FALSE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_COALESCING, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_REPLACING_ENTITY_REFERENCES, Boolean.TRUE);
        xmlInputFactory.setXMLResolver(new javax.xml.stream.XMLResolver()
                {
                @Override
                public Object     resolveEntity(String publicID, String systemID, String baseURI, String namespace)
                    {

                    return new java.io.ByteArrayInputStream(new byte[0]);
                    }
                });

        JAXBContext jaxbCtxt=JAXBContext.newInstance("gov.nih.nlm.ncbi.snp.docsum");
        this.unmarshaller=jaxbCtxt.createUnmarshaller();


        }
    private void run(String rsId) throws Exception
        {
    if(rsId.startsWith("rs")) rsId=rsId.substring(2);
        String uri="http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id="+rsId+"&retmode=xml";
            XMLEventReader reader= xmlInputFactory.createXMLEventReader(new StreamSource(uri)); 


            while(reader.hasNext())
                {
                XMLEvent evt=reader.peek();

                if(!evt.isStartElement())
                    {
                    reader.nextEvent();
                    continue;
                    }

                StartElement start=evt.asStartElement();
                String localName=start.getName().getLocalPart();

                if(!localName.equals("Rs"))
                    {
                    reader.nextEvent();
                    continue;
                    }

               Rs rs=unmarshaller.unmarshal(reader, Rs.class).getValue();

               for(Assembly as:rs.getAssembly())
                       {  
                        for(Component comp:as.getComponent())
                       {
                       for(MapLoc maploc: comp.getMapLoc())
                           {
                           System.out.print("rs"+rsId);
                           System.out.print("\t");
                           System.out.print(as.getGenomeBuild());
                           System.out.print("\t");
                           System.out.print(as.getGroupLabel());
                           System.out.print("\t");
                           System.out.print(comp.getChromosome());
                           System.out.print("\t");
                           System.out.print(maploc.getPhysMapInt());
                           System.out.println();
                           }
                           }
                           }
               }
            reader.close();
        }

    public static void main(String[] args)
        {
        try
            {
            Biostar95284 app=new Biostar95284();
            for(String arg:args)
                {
                app.run(arg);
                }
            }
        catch (Exception e)
            {
            e.printStackTrace();
            }
        }
    }

with :

javac Biostar95284.java

execute:

java Biostar95284 rs25 rs26
rs25    37.5    GRCh37.p10    7    11584141
rs25    37.5    HuRef    7    11442496
rs25    37.5    CRA_TCAGchr7v2    7    11637562
rs25    37.5    CHM1_1.0    7    11559989
rs26    37.5    GRCh37.p10    7    11583470
rs26    37.5    HuRef    7    11441825
rs26    37.5    CRA_TCAGchr7v2    7    11636891
rs26    37.5    CHM1_1.0    7    11559318

[burcakotlu]

Dear Pierre Lindenbaum,

Thanks for your answer. Although I have created the classes from the given xml schema using xjb successfully, the running the class Biostar95284 with given input data or any other data didn't give any output.

I have debugged the code and There are no found assembly. So it leaves the for loops. Any idea?

Thank you very much, Burcak

[Pierre Lindenbaum]

check your proxy. And sometimes, xjc is strange. In xmlInputFactory.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, Boolean.FALSE); try to replace Boolean.FALSE with Boolean.TRUE

[burcakotlu]

Replacing Boolean.FALSE with Boolean.TRUE works! Thank you. Burcak

[onemoreuser]

I have the same problem but replacing FALSE with TRUE doesn't solve the problem.