com.github.seqware.queryengine.plugins.contribs.MutationsToDonorsAggregationPlugin.java Source code

Introduction

Here is the source code for com.github.seqware.queryengine.plugins.contribs.MutationsToDonorsAggregationPlugin.java

Source

/*
 * Copyright (C) 2012 SeqWare
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package com.github.seqware.queryengine.plugins.contribs;

import com.github.seqware.queryengine.model.Feature;
import com.github.seqware.queryengine.model.FeatureSet;
import com.github.seqware.queryengine.model.Tag;
import com.github.seqware.queryengine.plugins.runners.MapperInterface;
import com.github.seqware.queryengine.plugins.runners.ReducerInterface;
import com.github.seqware.queryengine.plugins.recipes.FilteredFileOutputPlugin;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
import org.apache.hadoop.io.Text;

/**
 * This plug-in implements a quick and dirty export using Map/Reduce
 *
 * TODO: Copy from HDFS and parse key value file to VCF properly.
 *
 * @author dyuen
 * @version $Id: $Id
 */
public class MutationsToDonorsAggregationPlugin extends FilteredFileOutputPlugin {

    private Text text = new Text();
    private Text textKey = new Text();

    @Override
    public void map(long position, Map<FeatureSet, Collection<Feature>> atoms,
            MapperInterface<Text, Text> mapperInterface) {
        // map is mutation \t mutation ID ->   List of donor::project
        // "10:100008435-100008436_G->A   MU1157731" -> {"DO29264::LAML-KR","DO29242::LAML-KR","DO14015::COAD-US"}
        HashMap<String, ArrayList<String>> results = new HashMap<String, ArrayList<String>>();
        for (FeatureSet fs : atoms.keySet()) {
            for (Feature f : atoms.get(fs)) {

                if (f.getStart() != position) {
                    continue;
                }

                // create "10:100008435-100008436_G->A"
                String ref = null;
                String var = null;
                String id = null;
                // example of iterating through tags 
                for (Tag t : f.getTags()) {
                    if ("ref_base".equals(t.getKey())) {
                        ref = t.getValue().toString();
                    }
                    if ("call_base".equals(t.getKey())) {
                        var = t.getValue().toString();
                    }
                    if ("id".equals(t.getKey())) {
                        id = t.getValue().toString();
                    }
                }
                // varID becomes "10:100008435-100008436_G->A MU1157731"
                String varID = f.getSeqid() + ":" + f.getStart() + "-" + f.getStop() + "_" + ref + "->" + var + "\t"
                        + id;
                ArrayList<String> otherFS = results.get(varID);
                if (otherFS == null) {
                    otherFS = new ArrayList<String>();
                }
                // create DO29264::LAML-KR
                Tag tagByKey = fs.getTagByKey("donor");
                String donor = (String) tagByKey.getValue();
                tagByKey = fs.getTagByKey("project");
                String project = (String) tagByKey.getValue();
                String value = donor + "::" + project;
                if (!otherFS.contains(value)) {
                    otherFS.add(value);
                }
                results.put(varID, otherFS);
            }
        }
        // now iterate and emit into map/reduce 
        for (Entry<String, ArrayList<String>> entry : results.entrySet()) {
            boolean first = true;
            StringBuilder valueStr = new StringBuilder();
            for (String currFS : entry.getValue()) {
                if (first) {
                    first = false;
                    valueStr.append(currFS);
                } else {
                    valueStr.append(",").append(currFS);
                }
            }
            textKey.set(entry.getKey());
            text.set(entry.getKey() + "\t" + valueStr.toString());
            // ( "10:100008435-100008436_G->A MU1157731" , "10:100008435-100008436_G->A MU1157731 DO29264::LAML-KR,DO29242::LAML-KR,DO14015::COAD-US")
            mapperInterface.write(textKey, text);
        }
    }

    @Override
    public void reduce(Text key, Iterable<Text> values, ReducerInterface<Text, Text> reducerInterface) {
        // values 
        for (Text val : values) {
            String[] valArr = val.toString().split("\t");
            String[] fsArr = valArr[2].split(",");
            String newFeatStr = "";
            boolean first = true;
            for (String currFS : fsArr) {
                if (first) {
                    first = false;
                    newFeatStr += currFS;
                } else {
                    newFeatStr += "," + currFS;
                }
            }

            val.set(valArr[0] + "\t" + valArr[1] + "\t" + newFeatStr);
            reducerInterface.write(val, null);
        }
    }
}