es.uvigo.ei.sing.adops.operations.running.mrbayes.MrBayes3_2ProcessManager.java Source code

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Here is the source code for es.uvigo.ei.sing.adops.operations.running.mrbayes.MrBayes3_2ProcessManager.java

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/*-
 * #%L
 * ADOPS
 * %%
 * Copyright (C) 2012 - 2017 David Reboiro-Jato, Miguel Reboiro-Jato, Jorge Vieira, Florentino Fdez-Riverola, Cristina P. Vieira, Nuno A. Fonseca
 * %%
 * 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/gpl-3.0.html>.
 * #L%
 */
package es.uvigo.ei.sing.adops.operations.running.mrbayes;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.List;
import java.util.ListIterator;

import org.apache.commons.io.FileUtils;

import es.uvigo.ei.sing.adops.configuration.MrBayesConfiguration;
import es.uvigo.ei.sing.adops.datatypes.MrBayesOutput;
import es.uvigo.ei.sing.adops.operations.running.OperationException;

public class MrBayes3_2ProcessManager extends MrBayesDefaultProcessManager {
    private static final String[] SUPPORTED_VERSIONS = { "3.2.1", "3.2.2" };

    public MrBayes3_2ProcessManager(MrBayesConfiguration configuration) throws OperationException {
        super(configuration);
    }

    @Override
    public boolean isCompatibleWith(String version) {
        for (String supportedVersion : SUPPORTED_VERSIONS) {
            if (version.startsWith(supportedVersion))
                return true;
        }

        return false;
    }

    @Override
    public void buildSummary(MrBayesOutput output) throws OperationException {
        try {
            FileUtils.moveFile(new File(output.getConFile().getAbsolutePath() + ".tre"), output.getConFile());

            final List<String> lines = FileUtils.readLines(output.getConFile());
            final ListIterator<String> itLines = lines.listIterator();
            while (itLines.hasNext()) {
                final String line = itLines.next();

                if (line.contains("tree con_50_majrule")) {
                    final String[] lineSplit = line.split("=");
                    final String tree = lineSplit[1].trim();

                    itLines.set(lineSplit[0] + "= " + Newick.parse(tree.trim()));
                }
            }

            FileUtils.writeLines(output.getConFile(), lines);

            super.buildSummary(output);
        } catch (Exception e) {
            throw new OperationException("Error while working with consensus tree", e);
        }
    }

    @Override
    public void createMrBayesFile(MrBayesOutput output) throws OperationException {
        try (BufferedReader br = new BufferedReader(new FileReader(output.getNexusFile()));
                PrintWriter pw = new PrintWriter(output.getMrBayesFile())) {

            // Nexus data copying and nchar extraction
            pw.println(br.readLine());
            pw.println(br.readLine());

            final String ncharLine = br.readLine();
            pw.println(ncharLine);

            final int nchar = Integer.parseInt(ncharLine.split("nchar=")[1].split(";")[0]);

            String line;
            while ((line = br.readLine()) != null) {
                pw.println(line);
            }

            // MrBayes parameter creation
            pw.println("begin mrbayes;");
            pw.println("set autoclose=yes nowarn=yes;");
            pw.print("charset first_pos  = 1-");
            pw.print(nchar);
            pw.println("\\3;");
            pw.print("charset second_pos = 2-");
            pw.print(nchar);
            pw.println("\\3;");
            pw.print("charset third_pos  = 3-");
            pw.print(nchar);
            pw.println("\\3;");
            pw.println("partition by_codon = 3:first_pos,second_pos,third_pos;");
            pw.println("set partition=by_codon;");
            pw.println("lset nst=6 rates=invgamma;");
            pw.println("unlink shape=(3);");
            pw.print("mcmc ngen=");
            pw.print(this.configuration.getNumOfGenerations());
            pw.println(";");
            pw.print("sump burnin=");
            pw.print(this.configuration.getPBurnin());
            pw.println(";");
            pw.print("sumt conformat=simple burnin=");
            pw.print(this.configuration.getTBurnin());
            pw.println(";");
            pw.println("end;");
            pw.println();
            pw.flush();
        } catch (IOException ioe) {
            throw new OperationException(null, "Error creating MrBayes input file: " + output.getMrBayesFile(),
                    ioe);
        }
    }
}