SnpAnnotator.java

package plugins.snpannotator;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URL;
import java.net.URLConnection;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class SnpAnnotator
{

	public SnpAnnotator() throws IOException, InterruptedException
	{
		// String[] testIds = {"rs4637157"};

		String[] testIds = RsList.getRsList();

		System.out.println("SNP RS identifier\tClinical Association");
		for (String rs : testIds)
		{
			System.out.println(rs + "\t" + getNCBIannotation(rs));
			Thread.sleep(100);
		}

	}

	private String getNCBIannotation(String snpRsId) throws IOException
	{
		URL url = new URL("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=" + snpRsId);
		String bla = "";
		// URL yahoo = new URL("http://www.yahoo.com/");
		URLConnection yahooConnection = url.openConnection();
		BufferedReader in = new BufferedReader(new InputStreamReader(yahooConnection.getInputStream()));
		String inputLine;

		while ((inputLine = in.readLine()) != null)
		{

			Pattern p = Pattern
					.compile(".+<strong>Clinical Association:</strong></td><td  class=\"text10\" bgcolor=\"#f1f1f1\">(.+?)</td></TR>.+");

			Matcher m = p.matcher(inputLine);
			if (m.matches())
			{
				bla = m.group(1);
				break;
			}

		}
		in.close();

		return bla;
	}

	public static void main(String[] args) throws IOException, InterruptedException
	{
		new SnpAnnotator();
	}

}