root/trunk/plugins/zscore/org/pathvisio/plugins/statistics/IsDataInPathways.java @ 2979

// PathVisio,
// a tool for data visualization and analysis using Biological Pathways
// Copyright 2006-2009 BiGCaT Bioinformatics
//
// 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 org.pathvisio.plugins.statistics;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.bridgedb.IDMapperException;
import org.bridgedb.Xref;
import org.bridgedb.rdb.DataDerby;
import org.bridgedb.rdb.SimpleGdb;
import org.bridgedb.rdb.SimpleGdbFactory;
import org.pathvisio.data.XrefWithSymbol;
import org.pathvisio.debug.Logger;
import org.pathvisio.gex.GexManager;
import org.pathvisio.gex.ReporterData;
import org.pathvisio.gex.SimpleGex;
import org.pathvisio.preferences.PreferenceManager;
import org.pathvisio.util.FileUtils;
import org.pathvisio.util.PathwayParser;
import org.pathvisio.util.PathwayParser.ParseException;
import org.pathvisio.util.Utils;
import org.xml.sax.SAXException;
import org.xml.sax.XMLReader;
import org.xml.sax.helpers.XMLReaderFactory;

/**
 * Checks which genes from a dataset are not mapped in any pathway
 * Useful for targeted development of new pathways.
 *
 * TODO: make a plug-in out of this.
 */
public class IsDataInPathways
{

//      static File fGex = new File ("/home/martijn/uni-wrk/datasets/Starvation/Intestine/only_protemics_genmapp_format.pgex");
//      static File fGdb = new File ("/home/martijn/PathVisio-Data/gene databases/Mm_Derby_20080102.pgdb");
//      static File pwDir = new File ("/home/martijn/wikipathways/Mus_musculus");

        static File fGex = new File ("/media/KINGSTON/muscle_t12_vs_t0_PathVisio.pgex");
        static File fGdb = new File ("/home/martijn/PathVisio-Data/gene databases/Mm_Derby_20080102.pgdb");
        static File pwDir = new File ("/home/martijn/wikipathways/Mus_musculus");

        static File outFile = new File ("/home/martijn/Desktop/isdatainpahtways.txt");

        public static void main(String[] args) throws IDMapperException, ParseException, FileNotFoundException
        {
                PreferenceManager.init();
                GexManager gexManager = new GexManager();
                gexManager.setCurrentGex("" + fGex, false);

                XMLReader xmlReader;

                try
                {
                        xmlReader = XMLReaderFactory.createXMLReader();
                }
                catch (SAXException e)
                {
                        Logger.log.error("Problem while searching pathways", e);
                        return;
                }

                // read all rows of gex;
                SimpleGex gex = gexManager.getCurrentGex();

                Map<Xref, Xref> dataRefs = new HashMap<Xref, Xref>();
                Map<Xref, List<String>> counts = new HashMap<Xref, List<String>>();

                SimpleGdb gdb = SimpleGdbFactory.createInstance("" + fGdb, new DataDerby(), 0);

                for (int i = 0; i < gex.getNrRow(); ++i)
                {
                        ReporterData data = gex.getRow(i);
                        Xref src = data.getXref();
                        counts.put (src, new ArrayList<String>());
                        for (Xref dest : gdb.mapID(data.getXref()))
                        {
                                dataRefs.put (dest, src);
                        }
                        dataRefs.put (src, src);
                }

                for (File f : FileUtils.getFiles(pwDir, "gpml", false))
                {
                        PathwayParser pp = new PathwayParser (f, xmlReader);

                        for (XrefWithSymbol ref : pp.getGenes())
                        {
                                Xref ref2 = new Xref (ref.getId(), ref.getDataSource());
                                if (dataRefs.containsKey(ref2))
                                {
                                        counts.get(dataRefs.get(ref2)).add(pp.getName());
                                }
                        }
                }

                PrintStream out = new PrintStream(new FileOutputStream(outFile));
                for (int i = 0; i < gex.getNrRow(); ++i)
                {
                        ReporterData data = gex.getRow(i);
                        Xref ref = data.getXref();
                        String bpText = Utils.oneOf (gdb.getAttributes(ref, "Backpage"));
                        String desc = "";
                        if (bpText != null)
                        {
                                Pattern pat = Pattern.compile("<TH>Description:<TH>(.*)<TR>");
                                Matcher mat = pat.matcher (bpText);
                                if (mat.find())
                                {
                                        desc = mat.group(1);
                                }
                        }
                        List<String> pwyNames = counts.get(ref);
                        out.print (i + "\t" +
                                        ref.getId() + "\t" +
                                        ref.getDataSource().getSystemCode()  + "\t" +
                                        desc + "\t" +
                                        pwyNames.size() + "\t");

                        boolean first = true;
                        for (String name : pwyNames)
                        {
                                if (!first)
                                {
                                        out.print (" \\\\\\ ");
                                }
                                first = false;
                                out.print (name);
                        }
                        out.println();
                }
                out.close();
        }

}