public static void main(String[] args) throws Exception
	{
		BufferedReader reader = new BufferedReader(new FileReader(new File(
				ConfigReader.getMbqcDir() + File.separator + "dropbox" + File.separator + 
				"raw_design_matrix.txt")));
		
		BufferedWriter writer = new BufferedWriter(new FileWriter(new File(
				ConfigReader.getMbqcDir() + File.separator + "dropbox" + File.separator + 
				"huttenhower_raw_design_matrixPhylaAsColumns.txt")));
		
		String firstLine = reader.readLine();
		
		List<String> list = getPhylaHeaders(firstLine);

		writer.write("sample");
		for(String s : list)
			if( s != null)
				writer.write("\t" + s);
		
		writer.write("\n");
		
		int lastIndex =0;
		
		for( int x=0; x < list.size(); x++)
			if( list.get(x) != null)
				lastIndex = x;
		
		for(String s= reader.readLine(); s != null; s= reader.readLine())
		{
			if(  s.startsWith("chuttenhower"))
			{
				String[] splits = s.split("\t");
				writer.write(splits[0]);
				
				for( int x=0; x <= lastIndex; x++)
					if( list.get(x) != null)
						writer.write("\t" + splits[x] );
				
				writer.write("\n");
			}
		}
		
		writer.flush();  writer.close();
	}