it.iit.genomics.cru.bridges.liftover.ws.LiftOverRun.java Source code

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Here is the source code for it.iit.genomics.cru.bridges.liftover.ws.LiftOverRun.java

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/*******************************************************************************
 * Copyright 2014 Fondazione Istituto Italiano di Tecnologia
 * 
 * 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 and
 * limitations under the License.
 ******************************************************************************/
package it.iit.genomics.cru.bridges.liftover.ws;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ResourceBundle;

import org.apache.commons.lang.RandomStringUtils;

/**
 * 
 * @author Arnaud Ceol arnaud.ceol@iit.it
 *
 */

public class LiftOverRun {

    private static final ResourceBundle RESOURCE_BUNDLE = ResourceBundle.getBundle("/liftover");

    public static Mapping runLiftOver(String genome, String fromAssembly, String toAssembly, String chromosome,
            int start, int end) {

        String liftOverCommand = RESOURCE_BUNDLE.getString("liftOverCommand");

        String liftOverPath = RESOURCE_BUNDLE.getString("liftOverPath");

        String mapChainDir = RESOURCE_BUNDLE.getString("mapChainDir");

        String tmpDir = RESOURCE_BUNDLE.getString("tmpDir");

        Mapping mapping = null;

        Runtime r = Runtime.getRuntime();

        String rootFilename = String.format("%s", RandomStringUtils.randomAlphanumeric(8));

        String inputFilename = rootFilename + "-" + fromAssembly + ".bed";
        String outputFilename = rootFilename + "-" + toAssembly + ".bed";
        String unmappedFilename = rootFilename + "-" + "unmapped.bed";

        String mapChain = fromAssembly.toLowerCase() + "To" + toAssembly.toUpperCase().charAt(0)
                + toAssembly.toLowerCase().substring(1) + ".over.chain.gz";

        try {

            File tmpDirFile = new File(tmpDir);

            // if the directory does not exist, create it
            if (false == tmpDirFile.exists()) {
                System.out.println("creating directory: " + tmpDir);
                boolean result = tmpDirFile.mkdir();

                if (result) {
                    System.out.println("DIR created");
                }
            }

            // Write input bed file
            File inputFile = new File(tmpDir + inputFilename);
            // if file doesnt exists, then create it
            if (!inputFile.exists()) {
                inputFile.createNewFile();
            }

            FileWriter fw = new FileWriter(inputFile.getAbsoluteFile());
            BufferedWriter bw = new BufferedWriter(fw);
            bw.write(chromosome + "\t" + start + "\t" + end + "\n");
            bw.close();

            String commandArgs = String.format("%s %s %s %s %s", liftOverPath + "/" + liftOverCommand,
                    tmpDir + inputFilename, mapChainDir + mapChain, tmpDir + outputFilename,
                    tmpDir + unmappedFilename);
            System.out.println(commandArgs);

            Process p = r.exec(commandArgs);

            p.waitFor();

            BufferedReader b = new BufferedReader(new InputStreamReader(p.getInputStream()));
            String line = "";

            while ((line = b.readLine()) != null) {
                System.out.println(line);
            }
            b.close();

            b = new BufferedReader(new FileReader(tmpDir + outputFilename));

            while ((line = b.readLine()) != null) {
                String[] cells = line.split("\t");
                String newChromosome = cells[0];
                int newStart = Integer.parseInt(cells[1]);
                int newEnd = Integer.parseInt(cells[2]);
                mapping = new Mapping(genome, toAssembly, newChromosome, newStart, newEnd);
            }
            b.close();

            // delete
            File delete = new File(tmpDir + inputFilename);
            delete.delete();

            delete = new File(tmpDir + outputFilename);
            delete.delete();

            delete = new File(tmpDir + unmappedFilename);
            delete.delete();

        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (InterruptedException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }

        return mapping;
    }

}