Brush.KmerStatus.java Source code

Introduction

Here is the source code for Brush.KmerStatus.java

Source

/*
KmerStatus.java
2012  CloudBrush, developed by Chien-Chih Chen (rocky@iis.sinica.edu.tw), 
released under Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) 
at: https://github.com/ice91/CloudBrush
*/

package Brush;

import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import java.util.List;
import java.util.Map;

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.io.IntWritable;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.mapred.FileInputFormat;
import org.apache.hadoop.mapred.FileOutputFormat;
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.Reducer;
import org.apache.hadoop.mapred.Reporter;
import org.apache.hadoop.mapred.RunningJob;
import org.apache.hadoop.mapred.TextInputFormat;
import org.apache.hadoop.mapred.TextOutputFormat;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;
import org.apache.log4j.Logger;

public class KmerStatus extends Configured implements Tool {
    private static final Logger sLogger = Logger.getLogger(KmerStatus.class);

    public static class KmerStatusMapper extends MapReduceBase
            implements Mapper<LongWritable, Text, Text, IntWritable> {
        public void map(LongWritable lineid, Text txt, OutputCollector<Text, IntWritable> output, Reporter reporter)
                throws IOException {
            String vals[] = txt.toString().split("\t");
            output.collect(new Text(vals[1]), new IntWritable(1));
        }
    }

    public static class KmerStatusReducer extends MapReduceBase
            implements Reducer<Text, IntWritable, Text, IntWritable> {
        public void reduce(Text prefix, Iterator<IntWritable> iter, OutputCollector<Text, IntWritable> output,
                Reporter reporter) throws IOException {
            int sum = 0;
            while (iter.hasNext()) {
                sum += iter.next().get();
            }
            output.collect(prefix, new IntWritable(sum));
        }
    }

    public RunningJob run(String inputPath, String outputPath) throws Exception {
        sLogger.info("Tool name: KmerStatus");
        sLogger.info(" - input: " + inputPath);
        sLogger.info(" - output: " + outputPath);

        JobConf conf = new JobConf(KmerStatus.class);
        conf.setJobName("KmerStatus " + inputPath + " " + BrushConfig.K);
        // conf.setLong("AllKmer", allkmer);

        BrushConfig.initializeConfiguration(conf);

        FileInputFormat.addInputPath(conf, new Path(inputPath));
        FileOutputFormat.setOutputPath(conf, new Path(outputPath));

        conf.setInputFormat(TextInputFormat.class);
        conf.setOutputFormat(TextOutputFormat.class);

        conf.setMapOutputKeyClass(Text.class);
        conf.setMapOutputValueClass(IntWritable.class);

        conf.setOutputKeyClass(Text.class);
        conf.setOutputValueClass(IntWritable.class);

        //conf.setBoolean("mapred.output.compress", true);

        conf.setMapperClass(KmerStatusMapper.class);
        conf.setReducerClass(KmerStatusReducer.class);

        //delete the output directory if it exists already
        FileSystem.get(conf).delete(new Path(outputPath), true);

        return JobClient.runJob(conf);
    }

    public int run(String[] args) throws Exception {
        String inputPath = "";
        String outputPath = "";
        BrushConfig.K = 21;

        long starttime = System.currentTimeMillis();

        run(inputPath, outputPath);

        long endtime = System.currentTimeMillis();

        float diff = (float) (((float) (endtime - starttime)) / 1000.0);

        System.out.println("Runtime: " + diff + " s");

        return 0;
    }

    public static void main(String[] args) throws Exception {
        int res = ToolRunner.run(new Configuration(), new KmerStatus(), args);
        System.exit(res);
    }
}