Java tutorial
/** * Created on March 27, 2009. * * Copyright 2010- The MITRE Corporation. All rights reserved. * * Licensed under the Apache License, Version 2.0 (the "License"); you may not * use this file except in compliance with the License. You may obtain a copy of * the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the * License for the specific language governing permissions andlimitations under * the License. * * $Id$ */ package org.mitre.ccv.mapred; import java.io.IOException; import java.net.URL; import java.net.URLClassLoader; import java.util.ArrayList; import java.util.List; import java.util.Map; import java.util.NoSuchElementException; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configured; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.JobClient; import org.apache.hadoop.mapred.JobConf; import org.apache.hadoop.mapred.MapReduceBase; import org.apache.hadoop.mapred.Mapper; import org.apache.hadoop.mapred.OutputCollector; import org.apache.hadoop.mapred.Reporter; import org.apache.hadoop.mapred.SequenceFileInputFormat; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.hadoop.util.Tool; import org.apache.hadoop.util.ToolRunner; import org.mitre.mapred.io.StringDoublePairWritable; import org.mitre.mapred.fs.FileUtils; import org.mitre.ccv.mapred.io.KmerProbabilityMapWritable; /** * Map-reduce class for calculating the k-mer (n-gram) pi-values from the probabilities * generated by {@link CalculateKmerProbabilities} and processed by {@link InvertKmerProbabilities}. * * @author Marc Colosimo */ public class CalculateKmerPiValues extends Configured implements Tool { private static final Log LOG = LogFactory.getLog(CalculateKmerPiValues.class); /** * Mapper for calculating the Pi-value of a k-mer. */ public static class PiMapper extends MapReduceBase implements Mapper<Text, KmerProbabilityMapWritable, Text, StringDoublePairWritable> { private static final Log MAP_LOG = LogFactory.getLog(PiMapper.class); private StringDoublePairWritable pi = new StringDoublePairWritable(); public int start = CalculateKmerCounts.DEFAULT_START; public int end = CalculateKmerCounts.DEFAULT_END; @Override public void configure(JobConf job) { super.configure(job); start = Integer.parseInt(job.get(CalculateKmerCounts.START)); end = Integer.parseInt(job.get(CalculateKmerCounts.END)); LOG.debug("Configure: " + job); } public double getProb(Map<String, Double> map, String key) throws NoSuchElementException { if (!map.containsKey(key)) { throw new NoSuchElementException(key); } return map.get(key); } @Override public void map(Text key, KmerProbabilityMapWritable value, OutputCollector<Text, StringDoublePairWritable> output, Reporter reporter) throws IOException { String kmer = key.toString(); int windowSize = kmer.length(); if (windowSize < start) { //MAP_LOG.info("Skipping '" + kmer + "'. Length is to small."); return; } /** * We cannot check the length of the map because of things like 'AAA', * which only has 2 subsequences: 'A' and 'AA'. */ // This is quick and we generate a lot of status messages ! //reporter.setStatus("Calculating pi-value for " + kmer); Map<String, Double> map = value.get(); try { double p = this.getProb(map, kmer); double p1 = this.getProb(map, kmer.substring(0, windowSize - 1)); double p2 = this.getProb(map, kmer.substring(1, windowSize)); double p3 = this.getProb(map, kmer.substring(1, windowSize - 1)); double pe = (p1 * p2) / p3; pi.set(kmer, (p - pe) / pe, false); // set as global output.collect(key, pi); } catch (NoSuchElementException nsee) { MAP_LOG.fatal("Missing k-mer for " + kmer, nsee); throw new IOException( String.format("Missing kmer for '%s'.\n%s", key.toString(), nsee.getMessage())); } } } /** * Start up the job with the given parameters. * * @param jobConf {@link JobConf} to use * @param start starting window size * @param end ending window size * @param input path to the {@link SequenceFile}s * @param output path to save the output * @param cleanLogs if <code>true</code> remove the logs * @return exit status (0 if successful) * @throws java.lang.Exception * * @Todo: add the ability to just output as Doubles (add toString for StringDoublePairWritable) */ public int initJob(JobConf jobConf, int start, int end, String input, String output, boolean cleanLogs) throws Exception { JobConf conf = new JobConf(jobConf, CalculateKmerPiValues.class); conf.setJobName("CalculateKmerPiValues"); conf.set(CalculateKmerCounts.START, Integer.toString(start)); conf.set(CalculateKmerCounts.END, Integer.toString(end)); // Set up mapper SequenceFileInputFormat.setInputPaths(conf, new Path(input)); conf.setInputFormat(SequenceFileInputFormat.class); conf.setMapperClass(PiMapper.class); conf.setOutputKeyClass(Text.class); // final output key class conf.setOutputValueClass(StringDoublePairWritable.class); // final output value class // Uses default reducer (IdentityReducer) // @TODO: it would be nice to controll if we output to TextFile, // however StringDoublePairWritable outputs both k-mer and value conf.setOutputFormat(SequenceFileOutputFormat.class); SequenceFileOutputFormat.setOutputPath(conf, new Path(output)); JobClient.runJob(conf); if (cleanLogs) { LOG.info("removing log directory"); Path path = new Path(output, "_logs"); FileSystem fs = path.getFileSystem(jobConf); fs.delete(path, true); } return 0; } static int printUsage() { System.out.println( "CalculateKmerPiValues [-libjars <classpath,...>] [-m <maps>] [-r <reduces>] [-c] [-s <start>] [-e <end>] <input> <output>"); return -1; } @Override public int run(String[] args) throws Exception { JobConf conf = new JobConf(getConf()); boolean cleanLogs = false; Integer start = CalculateKmerCounts.DEFAULT_START; Integer end = CalculateKmerCounts.DEFAULT_END; List<String> other_args = new ArrayList<String>(); for (int i = 0; i < args.length; ++i) { try { if ("-m".equals(args[i])) { conf.setNumMapTasks(Integer.parseInt(args[++i])); } else if ("-r".equals(args[i])) { conf.setNumReduceTasks(Integer.parseInt(args[++i])); } else if ("-c".equals(args[i])) { cleanLogs = true; } else if ("-s".equals(args[i])) { start = Integer.parseInt(args[++i]); } else if ("-e".equals(args[i])) { end = Integer.parseInt(args[++i]); } else if ("-libjars".equals(args[i])) { conf.set("tmpjars", FileUtils.validateFiles(args[++i], conf)); URL[] libjars = FileUtils.getLibJars(conf); if (libjars != null && libjars.length > 0) { // Add libjars to client/tasks classpath conf.setClassLoader(new URLClassLoader(libjars, conf.getClassLoader())); // Adds libjars to our classpath Thread.currentThread().setContextClassLoader( new URLClassLoader(libjars, Thread.currentThread().getContextClassLoader())); } } else { other_args.add(args[i]); } } catch (NumberFormatException except) { System.out.println("ERROR: Integer expected instead of " + args[i]); return printUsage(); } catch (ArrayIndexOutOfBoundsException except) { System.out.println("ERROR: Required parameter missing from " + args[i - 1]); return printUsage(); } } // Make sure there are exactly 2 parameters left. if (other_args.size() != 2) { System.out.println("ERROR: Wrong number of parameters: " + other_args.size() + " instead of 2."); return printUsage(); } return initJob(conf, start, end, other_args.get(0), other_args.get(1), cleanLogs); } static public void main(String[] args) throws Exception { int res = ToolRunner.run(new Configuration(), new CalculateKmerPiValues(), args); System.exit(res); } }