it.iit.genomics.cru.simsearch.bundle.utils.PantherBridge.java Source code

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Here is the source code for it.iit.genomics.cru.simsearch.bundle.utils.PantherBridge.java

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/* 
 * Copyright 2017 Fondazione Istituto Italiano di Tecnologia.
 *
 * 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 it.iit.genomics.cru.simsearch.bundle.utils;

/**
 * @author Arnaud Ceol
 */
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;

import com.google.common.collect.ArrayListMultimap;

import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.methods.MultipartPostMethod;
import org.apache.commons.httpclient.methods.multipart.FilePart;

/**
 * Use panther webservice to get GO enrichment of a list of genes.
 * 
 * @author arnaudceol
 *
 */
public class PantherBridge {

    public final static int MAX_GENES_OUTPUT = 10;

    public static Collection<String[]> getEnrichment(String organism, String fileName, double threshold) {
        ArrayList<String[]> results = new ArrayList<>();

        ArrayListMultimap<String, String> genes = ArrayListMultimap.create();
        ArrayListMultimap<Double, String> pvalues = ArrayListMultimap.create();

        HashSet<String> uniqueGenes = new HashSet<>();

        try {
            String[] enrichmentTypes = { "process", "pathway" };

            for (String enrichmentType : enrichmentTypes) {

                HttpClient client = new HttpClient();
                MultipartPostMethod method = new MultipartPostMethod(
                        "http://pantherdb.org/webservices/garuda/tools/enrichment/VER_2/enrichment.jsp?");

                // Define name-value pairs to set into the QueryString
                method.addParameter("organism", organism);
                method.addParameter("type", "enrichment");
                method.addParameter("enrichmentType", enrichmentType); // "function",
                // "process",
                // "cellular_location",
                // "protein_class",
                // "pathway"
                File inputFile = new File(fileName);
                method.addPart(new FilePart("geneList", inputFile, "text/plain", "ISO-8859-1"));

                // PANTHER does not use the ID type
                // method.addParameter("IdType", "UniProt");

                // Execute and print response
                client.executeMethod(method);
                String response = method.getResponseBodyAsString();

                for (String line : response.split("\n")) {
                    if (false == "".equals(line.trim())) {

                        String[] row = line.split("\t");
                        // Id Name GeneId P-value
                        if ("Id".equals(row[0])) {
                            // header
                            continue;
                        }
                        // if (row.length > 1) {
                        String name = row[1];

                        String gene = row[2];
                        Double pvalue = Double.valueOf(row[3]);

                        uniqueGenes.add(gene);

                        if (pvalue < threshold) {
                            if (false == genes.containsKey(name)) {
                                pvalues.put(pvalue, name);
                            }
                            genes.put(name, gene);
                        }
                        // } else {
                        //    System.out.println("oups: " + row[0]);
                        // }
                    }
                }

                method.releaseConnection();
            }
            ArrayList<Double> pvalueList = new ArrayList<>();
            Collections.sort(pvalueList);

            pvalueList.addAll(pvalues.keySet());
            Collections.sort(pvalueList);

            int numGenes = uniqueGenes.size();

            for (Double pvalue : pvalueList) {
                for (String name : pvalues.get(pvalue)) {
                    String geneList = String.join(",", genes.get(name));
                    String result[] = { name, "" + pvalue, genes.get(name).size() + "/" + numGenes, geneList };
                    results.add(result);
                }
            }

        } catch (IOException e) {
            e.printStackTrace();
        }

        return results;
    }

    public static void main(String args[]) {
        Collection<String[]> results = PantherBridge.getEnrichment("Homo sapiens", "/tmp/genes.txt", 1);
        for (String[] result : results) {
            System.out.println(result[0] + " -> " + result[1] + " (" + result[2] + ")");
            ;
        }
    }

}