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

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Here is the source code for com.github.seqware.queryengine.plugins.contribs.GenesToDonorsAggregationPlugin.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 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 GenesToDonorsAggregationPlugin 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 gene -> List of donors::project
        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;
                }

                String id = null;
                String[] genes = null;
                for (Tag t : f.getTags()) {
                    if ("id".equals(t.getKey())) {
                        id = t.getValue().toString();
                    }
                    if ("EnsemblGene".equals(t.getKey())) {
                        genes = t.getValue().toString().split(",");
                    }
                }
                if (genes != null) {
                    for (String gene : genes) {
                        //String varID = f.getSeqid()+":"+f.getStart()+"-"+f.getStop()+"_"+ref+"->"+var+"\t"+id;
                        ArrayList<String> otherFS = results.get(gene);
                        if (otherFS == null) {
                            otherFS = new ArrayList<String>();
                        }
                        // need to convert SGID to hashed value
                        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(gene, otherFS);
                    }
                }
            }
        }
        // now iterate and add to results, currVar is gene
        for (String currVar : results.keySet()) {
            boolean first = true;
            StringBuilder valueStr = new StringBuilder();
            for (String currFS : results.get(currVar)) {
                if (first) {
                    first = false;
                    valueStr.append(currFS);
                } else {
                    valueStr.append(",").append(currFS);
                }
            }
            textKey.set(currVar); // key is gene
            text.set(valueStr.toString()); // value is list of donors
            mapperInterface.write(textKey, text);
        }
    }

    @Override
    public void reduce(Text key, Iterable<Text> values, ReducerInterface<Text, Text> reducerInterface) {
        // val are the values for a given gene, in this case it's a comma sep list
        String newFeatStr = "";
        boolean first = true;
        for (Text val : values) {
            String[] fsArr = val.toString().split(",");
            for (String currFS : fsArr) {
                if (first) {
                    first = false;
                    newFeatStr += currFS;
                } else {
                    newFeatStr += "," + currFS;
                }
            }
            // HELP, not sure what's going in here, why are you writing the text?
            //reducerInterface.write(val, text);
        }
        Text newVal = new Text();
        newVal.set(key.toString() + "\t" + newFeatStr);
        reducerInterface.write(newVal, null);
    }
}