http://www.biostars.org/post/show/45691/galaxy-taxonomy-output-to-newick-tree/

Biostar45691.java

import java.io.*;
import java.util.*;
import java.util.regex.*;

import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamWriter;

public class Biostar45691
	{
	private static class Node
		{
		int tax_id;
		int parent_id=-1;
		String name=null;
		int count=0;
		int count_leaf=0;
		@Override
		public int hashCode() {
			return tax_id;
			}
		@Override
		public boolean equals(Object obj) {
			return obj==this || ((Node)obj).tax_id==this.tax_id;
			}
		}
	private Map<Integer,Node> id2node=new HashMap<Integer, Biostar45691.Node>(898000);
		
	private void parseTaxonomy(File taxDir) throws Exception
		{
		Pattern pipe=Pattern.compile("[\\|]");
		BufferedReader in=new BufferedReader(new FileReader(new File(taxDir,"nodes.dmp")));
		String line;
		while((line=in.readLine())!=null)
			{
			String tokens[]=pipe.split(line,3);
			Node n=new Node();
			n.tax_id=Integer.parseInt(tokens[0].trim());
			n.parent_id=Integer.parseInt(tokens[1].trim());
			id2node.put(n.tax_id,n);
			}
		in.close();

		in=new BufferedReader(new FileReader(new File(taxDir,"names.dmp")));
		while((line=in.readLine())!=null)
			{
			String tokens[]=pipe.split(line);
			int tax_id=Integer.parseInt(tokens[0].trim());
			Node n=id2node.get(tax_id);
			if(n==null) continue;
			if(n.name==null || tokens[3].contains("scientific name"))
				{
				n.name=tokens[1].trim();
				}
			}
		in.close();
		}
	
	private void touch(Node n)
		{
		n.count++;
		if(n.parent_id!=n.tax_id)
			{
			Node p=id2node.get(n.parent_id);
			if(p!=null) touch(p);
			}
		}
	
	private void parseTaxonIds(File taxons) throws Exception
		{
		String line;
		BufferedReader in=new BufferedReader(new FileReader(taxons));
		while((line=in.readLine())!=null)
			{
			if(line.isEmpty()) continue;
			int taxon_id=Integer.parseInt(line.trim());
			Node n=id2node.get(taxon_id);
			if(n==null) continue;
			n.count_leaf++;
			touch(n);
			}
		in.close();
		}
	
	private Set<Node> lineage(Node n)
		{
		Set<Node> L=new HashSet<Node>();
		while(n!=null && n.tax_id!=n.parent_id)
			{
			L.add(n);
			n=id2node.get(n.parent_id);
			}
		return L;
		}
	
	private void dump(OutputStream out) throws Exception
		{
		XMLOutputFactory xmlfactory= XMLOutputFactory.newInstance();
		XMLStreamWriter w= xmlfactory.createXMLStreamWriter(out,"UTF-8");
		w.writeStartDocument("UTF-8","1.0");
		w.writeStartElement("gexf");
		w.writeAttribute("xmlns","http://www.gexf.net/1.2draft");
		w.writeAttribute("xmlns:xsi","http://www.w3.org/2001/XMLSchema-instance");
		w.writeAttribute("xsi:schemaLocation","http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd");
		
		w.writeAttribute("version","1.2");
		
		w.writeStartElement("meta");
		w.writeStartElement("creator");
		w.writeCharacters("Pierre Lindenbaum");
		w.writeEndElement();
		w.writeStartElement("description");
		w.writeCharacters("biostar 45691");
		w.writeEndElement();
		w.writeEndElement();
				
		w.writeStartElement("graph");
		w.writeAttribute("defaultedgetype","directed");
		
		w.writeStartElement("attributes");
		w.writeAttribute("class", "node");
		w.writeAttribute("mode", "static");
		
		w.writeStartElement("attribute");
		w.writeAttribute("id", "count");
		w.writeAttribute("title", "Count");
		w.writeAttribute("type", "float");
		w.writeEndElement();
		
		w.writeStartElement("attribute");
		w.writeAttribute("id", "countleaf");
		w.writeAttribute("title", "CountLeaf");
		w.writeAttribute("type", "float");
		w.writeEndElement();
		
		w.writeEndElement();
		
		
	
		Set<Node> toprint=new HashSet<Node>();
		for(Node n:this.id2node.values())
			{
			if(n.count==0) continue;
			if(toprint.addAll(lineage(n)));
			}
		
		w.writeStartElement("nodes");
		for(Node a:toprint)
			{
			w.writeStartElement("node");
			w.writeAttribute("id", String.valueOf(a.tax_id));
			w.writeAttribute("label",String.valueOf(a.name));
	
			w.writeStartElement("attvalues");
			
			w.writeStartElement("attvalue");
			w.writeAttribute("for","count");
			w.writeAttribute("value",String.valueOf(a.count));
			w.writeEndElement();	

			w.writeStartElement("attvalue");
			w.writeAttribute("for","countleaf");
			w.writeAttribute("value",String.valueOf(a.count_leaf));
			w.writeEndElement();	

			w.writeEndElement();
			w.writeEndElement();
			}
		w.writeEndElement();
		
		w.writeStartElement("edges");
		int L=0;
		for(Node a:toprint)
			{
			if(a.tax_id==a.parent_id) continue;
			w.writeStartElement("edge");
			w.writeAttribute("id",String.valueOf(++L));
			w.writeAttribute("source",String.valueOf(a.tax_id));
			w.writeAttribute("target",String.valueOf(a.parent_id));
			w.writeEndElement();
			}
		w.writeEndElement();
		
		w.writeEndElement();
		
		
		w.writeEndElement();
		w.writeEndDocument();
		w.flush();
		out.flush();
		}
	
	public static void main(String args[]) throws Exception
			{
			Biostar45691 app=new Biostar45691();
			
			if(args.length!=2)
				{
				System.err.println("Usage:  taxonomy-dir taxon-id-files");
				return;
				}
					
			app.parseTaxonomy(new File(args[0]));
			app.parseTaxonIds(new File(args[1]));
			app.dump(System.out);
			}
	}