edu.mda.bioinfo.ids.TcgaIdConverter.java Source code

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Here is the source code for edu.mda.bioinfo.ids.TcgaIdConverter.java

Source

/*
TcgaIdConverter 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 edu.mda.bioinfo.ids;

import java.io.File;
import java.io.IOException;
import java.util.TreeMap;
import java.util.TreeSet;
import org.apache.commons.io.FileUtils;

/**
 *
 * @author tdcasasent
 */
public class TcgaIdConverter {
    protected String mBaseDir = null;
    protected TreeMap<String, String> mMimatTOmirbase = null;
    protected TreeSet<String> mMaturemirs = null;
    protected TreeMap<String, String> mMirbaseTOgenesymbol = null;
    protected TreeMap<String, String> mEntreznumTOgenesymbol = null;
    protected TreeMap<String, String> mUcidTOgenesymbol = null;
    protected TreeMap<String, String> mOneToOne_ucidTOgenesymbol = null;
    protected TreeMap<String, String> mOneToOne_genesymbolToucid = null;
    protected TreeMap<String, TreeSet<String>> mGeneSynonyms = null;

    public TcgaIdConverter(String theBaseDir) {
        System.out.println("TcgaIdConvert 2015-12-23-1045");
        mBaseDir = theBaseDir;
    }

    public void getAndPrepFiles() throws IOException, Exception {
        System.out.println("getAndPrepFiles start");
        File downloadDir = new File(mBaseDir, "downloads");
        System.out.println("getAndPrepFiles clear download dir");
        FileUtils.deleteQuietly(downloadDir);
        System.out.println("getAndPrepFiles make download dir");
        downloadDir.mkdir();
        System.out.println("getAndPrepFiles DownloadFiles");
        DownloadFiles df = new DownloadFiles(downloadDir.getAbsolutePath());
        df.downloadFiles();
        System.out.println("getAndPrepFiles UncompressFiles");
        UncompressFiles uf = new UncompressFiles(downloadDir.getAbsolutePath());
        uf.uncompressFiles();
        System.out.println("getAndPrepFiles PrepFiles");
        PrepFiles pf = new PrepFiles(downloadDir.getAbsolutePath());
        pf.prepFiles();
        System.out.println("getAndPrepFiles done");
    }

    public void loadFiles() throws IOException, Exception {
        System.out.println("TcgaIdConverter::loadFiles start");
        File downloadDir = new File(mBaseDir, "downloads");
        LoadFiles lf = new LoadFiles(downloadDir.getAbsolutePath());
        lf.loadFiles();
        mMimatTOmirbase = lf.mMimatTOmirbase;
        mMaturemirs = lf.mMaturemirs;
        mMirbaseTOgenesymbol = lf.mMirbaseTOgenesymbol;
        mEntreznumTOgenesymbol = lf.mEntreznumTOgenesymbol;
        mUcidTOgenesymbol = lf.mUcidTOgenesymbol;
        mOneToOne_ucidTOgenesymbol = lf.mOneToOne_ucidTOgenesymbol;
        mOneToOne_genesymbolToucid = lf.mOneToOne_genesymbolToucid;
        mGeneSynonyms = lf.mGeneSynonyms;
        System.out.println("TcgaIdConverter::loadFiles done");
    }

    public String convert_mimat_TO_mirbase(String theMimat) {
        return mMimatTOmirbase.get(theMimat);
    }

    public boolean is_mature_mirbase(String theMirbase) {
        return mMaturemirs.contains(theMirbase);
    }

    public String convert_mirbase_TO_genesymbol(String theMirbase) {
        return mMirbaseTOgenesymbol.get(theMirbase);
    }

    public String convert_entreznum_TO_genesymbol(String theEntrezNum) {
        return mEntreznumTOgenesymbol.get(theEntrezNum);
    }

    public String convert_ucid_TO_genesymbol(String theUcId) {
        return mUcidTOgenesymbol.get(theUcId);
    }

    public String convert_oneToOne_ucid_TO_genesymbol(String theUcId) {
        return mOneToOne_ucidTOgenesymbol.get(theUcId);
    }

    public String convert_oneToOne_genesymbol_TO_ucid(String theGeneSymbol) {
        return mOneToOne_genesymbolToucid.get(theGeneSymbol);
    }

    public String[] get_oneToOne_ucid_list() {
        return mOneToOne_ucidTOgenesymbol.keySet().toArray(new String[0]);
    }

    public String[] get_oneToOne_genesymbol_list() {
        return mOneToOne_genesymbolToucid.keySet().toArray(new String[0]);
    }

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        try {
            //String baseDir = "/Users/tdcasasent/development/TcgaIdConverter";
            String baseDir = args[0];
            TcgaIdConverter tic = new TcgaIdConverter(baseDir);
            tic.getAndPrepFiles();
            tic.loadFiles();
        } catch (Exception exp) {
            exp.printStackTrace(System.err);
        }
    }
}