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

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Here is the source code for org.mda.bcb.tcgagsdata.create.ReadPlatform.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.TreeMap;
import java.util.TreeSet;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.filefilter.TrueFileFilter;
import org.apache.commons.io.filefilter.WildcardFileFilter;
import org.mda.bcb.tcgagsdata.GSStringUtils;
import org.mda.bcb.tcgagsdata.TcgaGSData;

/**
 *
 * @author tdcasasent
 */
public class ReadPlatform {
    public String mReadPath = null;
    public String mWriteFile = null;
    public int mNumberOfGenes = 0;
    public int mNumberOfSamples = 0;
    public double[][] mGenesBySamplesValues = null;
    public String[] mSamples = null;
    public String[] mGenes = null;

    public ReadPlatform(String theReadPath, String theWriteFile) {
        TcgaGSData.printVersion();
        mReadPath = theReadPath;
        mWriteFile = theWriteFile;
    }

    public void readPlatform(String thePlatform) throws IOException, Exception {
        TcgaGSData.printWithFlag("readPlatform for " + thePlatform + " beginning");
        TcgaGSData.printWithFlag("readPlatform can consume excessive amounts of time and memory");
        mNumberOfGenes = 0;
        TreeMap<String, Integer> geneMap = null;
        {
            ReadPlatform_GeneEq lg = new ReadPlatform_GeneEq(mReadPath);
            lg.getNamesGenes(thePlatform);
            mGenes = lg.mGenes;
            geneMap = TcgaGSData.buildIndexMap(lg.mGenes);
            mNumberOfGenes = lg.mSize;
        }
        mNumberOfSamples = 0;
        boolean found = false;
        long start = System.currentTimeMillis();
        TreeSet<File> dataFileList = new TreeSet<>();
        dataFileList.addAll(FileUtils.listFiles(new File(mReadPath, thePlatform),
                new WildcardFileFilter("matrix_data_*.tsv"), TrueFileFilter.INSTANCE));
        for (File input : dataFileList) {
            try (BufferedReader br = Files.newBufferedReader(Paths.get(input.getAbsolutePath()),
                    Charset.availableCharsets().get("ISO-8859-1"))) {
                found = true;
                TcgaGSData.printWithFlag("readPlatform file=" + input.getAbsolutePath());
                // first line samples
                String line = br.readLine();
                TreeMap<String, Integer> sampleMap = TcgaGSData
                        .buildIndexMap(GSStringUtils.afterTab(line).split("\t", -1));
                if (0 == mNumberOfSamples) {
                    mSamples = GSStringUtils.afterTab(line).split("\t", -1);
                    mNumberOfSamples = mSamples.length;
                    mGenesBySamplesValues = new double[mNumberOfGenes][mNumberOfSamples];
                } else {
                    if (mNumberOfSamples != GSStringUtils.afterTab(line).split("\t", -1).length) {
                        throw new Exception("Expected sample count of " + mNumberOfSamples + " but found different "
                                + input.getAbsolutePath());
                    }
                }
                line = br.readLine();
                while (null != line) {
                    String gene = GSStringUtils.beforeTab(line);
                    Integer intIndex = geneMap.get(gene);
                    if (null != intIndex) {
                        int geneIndex = intIndex;
                        double[] valueList = convertToDouble(GSStringUtils.afterTab(line).split("\t", -1));
                        for (int x = 0; x < valueList.length; x++) {
                            int sampleIndex = sampleMap.get(mSamples[x]);
                            mGenesBySamplesValues[geneIndex][sampleIndex] = valueList[x];
                        }
                    } else {
                        throw new Exception(
                                "readPlatform for " + thePlatform + " found unexpected 'gene' = " + gene);
                    }
                    line = br.readLine();
                }
            }
        }
        long finish = System.currentTimeMillis();
        TcgaGSData.printWithFlag(
                "readPlatform for " + thePlatform + " retrieved in " + ((finish - start) / 1000.0) + " seconds");
        if (false == found) {
            throw new Exception("readPlatform for " + thePlatform + " not found");
        } else {
            TcgaGSData.printWithFlag("write " + thePlatform + " to " + mWriteFile);
            writeFile();
        }
    }

    protected void writeFile() throws IOException {
        TcgaGSData.printWithFlag("writeFile " + mWriteFile);
        try (BufferedWriter bw = Files.newBufferedWriter(Paths.get(mWriteFile),
                Charset.availableCharsets().get("ISO-8859-1"))) {
            // write header of samples
            for (String sample : mSamples) {
                bw.write("\t" + sample);
            }
            bw.newLine();
            // write rows
            for (int index = 0; index < mNumberOfGenes; index++) {
                // write gene
                bw.write(mGenes[index]);
                // write data
                for (double data : mGenesBySamplesValues[index]) {
                    bw.write("\t" + data);
                }
                bw.newLine();
            }
        }
        TcgaGSData.printWithFlag("writeFile finished");
    }

    protected double[] convertToDouble(String[] theStrings) {
        double[] doubleArray = new double[theStrings.length];
        for (int x = 0; x < theStrings.length; x++) {
            String myStr = theStrings[x];
            if ("NA".equalsIgnoreCase(myStr)) {
                doubleArray[x] = Double.NaN;
            } else if ("NaN".equalsIgnoreCase(myStr)) {
                doubleArray[x] = Double.NaN;
            } else {
                doubleArray[x] = Double.parseDouble(myStr);
            }
        }
        return doubleArray;
    }
}