edu.berkeley.compbio.phyloutils.NearestNodeFinder.java Source code

Introduction

Here is the source code for edu.berkeley.compbio.phyloutils.NearestNodeFinder.java

Source

/*
 * Copyright (c) 2006-2013  David Soergel  <dev@davidsoergel.com>
 * Licensed under the Apache License, Version 2.0
 * http://www.apache.org/licenses/LICENSE-2.0
 */

package edu.berkeley.compbio.phyloutils;

import com.davidsoergel.conja.Function;
import com.davidsoergel.conja.Parallel;
import com.davidsoergel.dsutils.file.IntArrayReader;
import com.davidsoergel.trees.NoSuchNodeException;
import org.apache.commons.collections15.iterators.ArrayIterator;

import java.io.IOException;
import java.io.PrintWriter;
import java.util.Map;

/**
 * Load a list of "known" nodes, eg the isolates.  Then for each query sequence (eg from an environment), find the
 * closest known node, and print the distance (along with whatever other stats are desired, e.g. subtree span).
 *
 * @author <a href="mailto:dev@davidsoergel.com">David Soergel</a>
 * @version $Id$
 */
public class NearestNodeFinder {
    static HugenholtzTaxonomyService service = new HugenholtzTaxonomyService();

    public static void main(String[] argv) throws IOException, NoSuchNodeException {
        //service.setGreengenesRawFilename(argv[0]);
        service.setHugenholtzFilename(argv[0]);
        //service.setSynonymService(NcbiTaxonomyClient.getInstance());
        service.init();

        final int[] targetIds = IntArrayReader.read(argv[1]);
        int[] queryIds = IntArrayReader.read(argv[2]);
        final double minDistance = Double.parseDouble(argv[3]); // implement leave-one-out at any level

        Map<Integer, Double> results = Parallel.map(new ArrayIterator(queryIds), new Function<Integer, Double>() {
            public Double apply(Integer queryId) {
                try {
                    double best = Double.MAX_VALUE;
                    for (int targetId : targetIds) {
                        double d = service.minDistanceBetween(queryId, targetId);
                        if (d >= minDistance) {
                            best = Math.min(best, d);
                        }
                    }
                    return best;
                } catch (NoSuchNodeException e) {
                    throw new Error(e);
                }
            }
        });

        String outfileName = argv[4];
        PrintWriter out = new PrintWriter(outfileName);
        out.println("id\tdist");

        for (Map.Entry<Integer, Double> entry : results.entrySet()) {
            out.println(entry.getKey() + "\t" + entry.getValue());
        }
        out.close();
    }
}