org.mda.bcb.tcgagsdata.create.Compilation.java Source code

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Here is the source code for org.mda.bcb.tcgagsdata.create.Compilation.java

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/*
TcgaGSData Copyright 2014, 2015, 2016 University of Texas MD Anderson Cancer Center
    
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 2 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 org.mda.bcb.tcgagsdata.create;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.TreeSet;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.filefilter.FileFilterUtils;
import org.apache.commons.io.filefilter.TrueFileFilter;
import org.mda.bcb.tcgagsdata.GSStringUtils;
import org.mda.bcb.tcgagsdata.TcgaGSData;

/**
 *
 * @author tdcasasent
 */
public class Compilation {
    public String mClinicalDir = null;
    public String mInputFiles = null;
    public String mOutputFile = null;

    public Compilation(String theClinicalDir, String theInputFiles, String theOutputFile) {
        mClinicalDir = theClinicalDir;
        mInputFiles = theInputFiles;
        mOutputFile = theOutputFile;
    }

    protected ArrayList<String> getHeaders(Collection<File> theFiles) throws IOException {
        TcgaGSData.printWithFlag("Compilation::getHeaders");
        ArrayList<String> headers = new ArrayList<>();
        for (File clinFile : theFiles) {
            try (BufferedReader br = Files.newBufferedReader(Paths.get(clinFile.getAbsolutePath()),
                    Charset.availableCharsets().get("ISO-8859-1"))) {
                String line = br.readLine();
                String[] hdrs = line.split("\t", -1);
                for (String hdr : hdrs) {
                    if ((null != hdr) && (false == "".equals(hdr))) {
                        if (false == headers.contains(hdr)) {
                            headers.add(hdr);
                        }
                    }
                }
            }
        }
        return headers;
    }

    public void process() throws IOException, Exception {
        TcgaGSData.printWithFlag("Compilation::process - mClinicalDir=" + mClinicalDir);
        TcgaGSData.printWithFlag("Compilation::process - mInputFiles=" + mInputFiles);
        TcgaGSData.printWithFlag("Compilation::process - mOutputFile=" + mOutputFile);
        Collection<File> results = FileUtils.listFiles(new File(mClinicalDir),
                FileFilterUtils.nameFileFilter(mInputFiles), TrueFileFilter.INSTANCE);
        ArrayList<String> headers = getHeaders(results);
        TreeSet<String> patients = new TreeSet<>();
        TreeSet<String> lines = new TreeSet<>();
        String headerLine = null;
        for (String header : headers) {
            if (null == headerLine) {
                headerLine = header;
            } else {
                headerLine = headerLine + "\t" + header;
            }
        }
        boolean headersNeeded = true;
        for (File clinFile : results) {
            TcgaGSData.printWithFlag("Compilation::process - clinFile=" + clinFile.getAbsolutePath());
            try (BufferedReader br = Files.newBufferedReader(Paths.get(clinFile.getAbsolutePath()),
                    Charset.availableCharsets().get("ISO-8859-1"))) {
                String line = br.readLine();
                ArrayList<String> currentHeaders = new ArrayList<>();
                currentHeaders.addAll(Arrays.asList(line.split("\t", -1)));
                for (line = br.readLine(); null != line; line = br.readLine()) {
                    String newLine = null;
                    String[] splitted = line.split("\t", -1);
                    for (String header : headers) {
                        String token = "NA";
                        int index = currentHeaders.indexOf(header);
                        if (index > -1) {
                            token = splitted[index];
                        }
                        if (null == newLine) {
                            newLine = token;
                        } else {
                            newLine = newLine + "\t" + token;
                        }
                    }
                    lines.add(newLine);
                    String patient = GSStringUtils.beforeTab(newLine);
                    if (false == patients.add(patient)) {
                        throw new Exception("ERROR - patient duplicated " + patient);
                    }
                }
            }
        }
        try (BufferedWriter bw = Files.newBufferedWriter(Paths.get(mOutputFile),
                Charset.availableCharsets().get("ISO-8859-1"))) {
            bw.write(headerLine);
            bw.newLine();
            for (String line : lines) {
                bw.write(line);
                bw.newLine();
            }
        }
    }
}