http://biostar.stackexchange.com/questions/3872

gistfile1.txt

import gov.nih.nlm.ncbi.snp.geno.Individual;
import gov.nih.nlm.ncbi.snp.geno.SnpInfo;

import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.zip.GZIPInputStream;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.Unmarshaller;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;


//xjc -d . ftp://ftp.ncbi.nlm.nih.gov/snp/specs/genoex_1_5.xsd
public class Biostar3872
	{
		
	private void run() throws Exception
		{
		
		
		XMLInputFactory xmlInputFactory = XMLInputFactory.newInstance();
		xmlInputFactory.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, Boolean.TRUE);
		xmlInputFactory.setProperty(XMLInputFactory.IS_COALESCING, Boolean.TRUE);
		xmlInputFactory.setProperty(XMLInputFactory.IS_REPLACING_ENTITY_REFERENCES, Boolean.TRUE);
		String chroms[]={
				"1","2","3","4","5","6","7","8","9",
				"10","11","12","13","14","15","16","17","18","19",
				"AltOnly","MT","Multi","NotOn","Un","X","Y"};
		JAXBContext jaxbCtxt=JAXBContext.newInstance(Individual.class,SnpInfo.class);
		Unmarshaller unmarshaller=jaxbCtxt.createUnmarshaller();
		
		for(String chrom:chroms)
			{
			List<String> headers=new ArrayList<String>();
			HashMap<Integer, Integer> column2id=new HashMap<Integer, Integer>();
			
			URL url=new URL("ftp://ftp.ncbi.nih.gov/snp/organisms/mouse_10090/genotype/gt_chr"+chrom+".xml.gz");
			System.err.println("Parsing "+url);
			XMLEventReader reader= xmlInputFactory.createXMLEventReader(new GZIPInputStream(url.openStream()));	
			boolean headerPrinted=false;
			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("Individual"))
					{
					Individual indi=unmarshaller.unmarshal(reader, Individual.class).getValue();
					for(Individual.SourceInfo sourceInfo:indi.getSourceInfo())
						{
						column2id.put(headers.size(), indi.getIndId());
						headers.add(sourceInfo.getIndId());
						break;
						}
					
					}
				else if(localName.equals("SnpInfo"))
					{
					SnpInfo snpInfo=unmarshaller.unmarshal(reader, SnpInfo.class).getValue();
					HashMap<Integer, String> indId2genotypes=new HashMap<Integer, String>();
					for(SnpInfo.SsInfo ssInfo:snpInfo.getSsInfo())
						{
						for(SnpInfo.SsInfo.ByPop byPop:ssInfo.getByPop())
							{
							for(SnpInfo.SsInfo.ByPop.GTypeByInd gtype:byPop.getGTypeByInd())
								{
								indId2genotypes.put(gtype.getIndId(), gtype.getGtype());
								}
							}
						}
					
					if(!headerPrinted)
						{
						headerPrinted=true;
						System.out.print("rs##\tPosition");
						for(String s:headers)
							{
							System.out.print("\t"+s);
							}
						System.out.println();
						}
					
					System.out.print("rs"+snpInfo.getRsId());
					System.out.print("\t");
					for(SnpInfo.SnpLoc loc:snpInfo.getSnpLoc())
						{
						System.out.print("chrom"+loc.getChrom()+":"+loc.getStart()+"("+loc.getGenomicAssembly()+");");
						}
					for(int i=0;i< headers.size();++i)
						{
						Integer indiId=column2id.get(i);
						String gtype=indId2genotypes.get(indiId);
						if(gtype==null) gtype="#NA";
						System.out.print("\t"+gtype);
						}
					System.out.println();
					}
				else
					{
					//flush event
					reader.nextEvent();
					}
				}
			reader.close();
			}
		}
	public static void main(String[] args)
		{
		try
			{
			new Biostar3872().run();
			}
		catch (Exception e)
			{
			e.printStackTrace();
			}
		}
	}