nl.systemsgenetics.genenetworkbackend.div.CreateCgdMatrix.java Source code

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Here is the source code for nl.systemsgenetics.genenetworkbackend.div.CreateCgdMatrix.java

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package nl.systemsgenetics.genenetworkbackend.div;

import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;

/**
 *
 * @author patri
 */
public class CreateCgdMatrix {

    /**
     * @param args the command line arguments
     * @throws java.io.FileNotFoundException
     */
    public static void main(String[] args) throws FileNotFoundException, IOException {

        final File cgdFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\CGD.txt");
        final File cgdMatrixFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\CGD_matrix.txt");

        final CSVParser parser = new CSVParserBuilder().withSeparator('\t').withIgnoreQuotations(true).build();
        final CSVReader reader = new CSVReaderBuilder(new BufferedReader(new FileReader(cgdFile))).withSkipLines(1)
                .withCSVParser(parser).build();

        HashSet<String> cgdInfo = new HashSet<>(30);
        cgdInfo.add("AD");
        cgdInfo.add("AD");
        cgdInfo.add("XL");
        cgdInfo.add("Pediatric");

        HashMap<String, HashSet<String>> geneInfoMap = new HashMap<>();

        String[] nextLine;
        while ((nextLine = reader.readNext()) != null) {

            HashSet<String> geneInfo = new HashSet<>();
            geneInfoMap.put(nextLine[0], geneInfo);

            String diseaseManifistationField = nextLine[7];
            String[] diseaseManifistations = StringUtils.split(diseaseManifistationField, ';');

            geneInfo.add(nextLine[4].trim());
            geneInfo.add(nextLine[5].trim());

            for (int i = 0; i < diseaseManifistations.length; ++i) {

                diseaseManifistations[i] = diseaseManifistations[i].trim();
                cgdInfo.add(diseaseManifistations[i]);
                geneInfo.add(diseaseManifistations[i]);

            }

        }

        cgdInfo.remove("General");

        DoubleMatrixDataset<String, String> cgdInfoTable = new DoubleMatrixDataset<>(geneInfoMap.keySet(), cgdInfo);

        for (Map.Entry<String, HashSet<String>> geneInfoEntry : geneInfoMap.entrySet()) {

            String gene = geneInfoEntry.getKey();
            HashSet<String> geneInfo = geneInfoEntry.getValue();

            for (String geneProperty : geneInfo) {

                if (cgdInfoTable.containsCol(geneProperty)) {
                    cgdInfoTable.setElement(gene, geneProperty, 1);
                }

            }

        }

        cgdInfoTable.save(cgdMatrixFile);

    }

}