diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/mapping/ORApathwayEnrichment.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/mapping/ORApathwayEnrichment.java
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+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/mapping/ORApathwayEnrichment.java
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+package fr.inrae.toulouse.metexplore.met4j_toolbox.mapping;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioPathway;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.FBCParser;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.GroupPathwayParser;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.NotesParser;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.PackageParser;
+import fr.inrae.toulouse.metexplore.met4j_mapping.Mapper;
+import fr.inrae.toulouse.metexplore.met4j_mapping.enrichment.PathwayEnrichment;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumParameterTypes;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.Format;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.ParameterType;
+import org.kohsuke.args4j.Option;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.*;
+import java.util.stream.Collectors;
+
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Sbml;
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Tsv;
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumParameterTypes.InputFile;
+
+public class ORApathwayEnrichment extends AbstractMet4jApplication {
+
+
+ @Option(name = "-th", aliases = {"--threshold"}, usage = "threshold to select significant pathways. No filtering if <=0")
+ public double th = 0.0;
+
+ @Format(name = Sbml)
+ @ParameterType(name = InputFile)
+ @Option(name = "-s", aliases = {"--sbml"}, usage = "Input model : SBML file with pathway annotation", required = true)
+ public String sbml;
+
+ @ParameterType(name = InputFile)
+ @Format(name = Tsv)
+ @Option(name = "-i", aliases = {"--data"}, usage = "Input data : Compounds of interest file, as one SBML specie identifier per line", required = true)
+ public String input;
+
+ @ParameterType(name= EnumParameterTypes.OutputFile)
+ @Format(name= EnumFormats.Tsv)
+ @Option(name = "-o", aliases = {"--output"}, usage = "Output file : tabulated file with pathway identifier, pathway name, adjusted p-value.", required=true)
+ public String outputFile;
+
+ enum correction {Bonferroni, BenjaminiHochberg, HolmBonferroni}
+ @Option(name = "-c", aliases = {"--correction"}, usage = "Method for multiple testing p-value adjustment.")
+ public correction corr = correction.BenjaminiHochberg;
+
+
+ /**
+ * <p>readSbml.</p>
+ *
+ * @return a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork} object.
+ */
+ protected Map<String, List<String>> readSbml() {
+ JsbmlReader reader = new JsbmlReader(this.sbml);
+
+ BioNetwork bn = null;
+ Map<String,List<String>> names = new HashMap<>();
+ try {
+ bn = reader.read();
+ } catch (Met4jSbmlReaderException e) {
+ e.printStackTrace();
+ System.err.println("Problem while reading the sbml file " + this.sbml);
+ System.exit(1);
+ }
+
+ for(BioMetabolite m : bn.getMetabolitesView()){
+ names.computeIfAbsent(m.getName(), k -> new ArrayList<>()).add(m.getId());
+ }
+ return names;
+
+ }
+
+ public static void main(String[] args) {
+ ORApathwayEnrichment app = new ORApathwayEnrichment();
+
+ app.parseArguments(args);
+
+ app.run();
+ }
+
+ private void run() {
+ //open file
+ FileWriter fw = null;
+ try {
+ fw = new FileWriter(outputFile);
+ } catch (IOException e) {
+ System.err.println("Error while opening the output file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+
+ //import network
+ System.out.print("Reading SBML...");
+ JsbmlReader reader = new JsbmlReader(this.sbml);
+ ArrayList<PackageParser> pkgs = new ArrayList<>(Arrays.asList(
+ new NotesParser(false), new FBCParser(), new GroupPathwayParser()));
+
+ BioNetwork network = null;
+ try {
+ network = reader.read(pkgs);
+ } catch (Met4jSbmlReaderException e) {
+ System.err.println("Error while reading the SBML file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ System.out.println(" Done.");
+
+ //import data
+ System.out.println("Import data...");
+ Mapper<BioMetabolite> metMapper = new Mapper<>(network, BioNetwork::getMetabolitesView).skipIfNotFound();
+ HashSet<BioMetabolite> noi = null;
+ try {
+ noi = new HashSet<>(metMapper.map(input));
+ } catch (IOException e) {
+ System.err.println("Error while reading the compound of interest file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ if (metMapper.getNumberOfSkippedEntries() > 0)
+ System.err.println(metMapper.getNumberOfSkippedEntries() + " compounds not found in network.");
+ System.out.println(noi.size() + " compounds imported.");
+ System.out.println(" Done.");
+
+ //Run analysis
+ System.out.print("Perform Pathway Enrichment...");
+ int corrInt;
+ switch(corr)
+ {
+ case BenjaminiHochberg:
+ corrInt = PathwayEnrichment.BENJAMINIHOCHBERG;
+ break;
+ case HolmBonferroni:
+ corrInt = PathwayEnrichment.HOLMBONFERRONI;
+ break;
+ case Bonferroni:
+ corrInt = PathwayEnrichment.BONFERRONI;
+ break;
+ default:
+ corrInt = PathwayEnrichment.BENJAMINIHOCHBERG;
+ break;
+ }
+ PathwayEnrichment pe = new PathwayEnrichment(network,noi);
+ Map<BioPathway, Double> pathwayScore = pe.computeEnrichment(corrInt);
+ System.out.println(" Done.");
+
+ //filter
+ if(th>0.0){
+ System.out.println("Select significant pathways...");
+ pathwayScore = pathwayScore.entrySet().stream().filter(e -> e.getValue()<=th).collect(Collectors.toMap(e->e.getKey(),e->e.getValue()));
+ System.out.println("\t"+pathwayScore.size()+" significant pathways found.");
+ System.out.println(" Done.");
+ }
+
+ //export
+ System.out.println("Export results...");
+ try {
+ for (Map.Entry<BioPathway, Double> e : pathwayScore.entrySet()) {
+ BioPathway m = e.getKey();
+ fw.write(m.getId() + "\t" + m.getName() + "\t" + e.getValue() + "\n");
+ }
+ fw.close();
+ } catch (IOException e) {
+ System.err.println("Error while writing the result file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ System.out.println("done.");
+
+
+ }
+
+
+ @Override
+ public String getLabel() {
+ return this.getClass().getSimpleName();
+ }
+
+ @Override
+ public String getLongDescription() {
+ return "Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.";
+ }
+
+ @Override
+ public String getShortDescription() {
+ return "Perform Over Representation Analysis for Pathway Enrichment, using one-tailed exact Fisher Test.\n" +
+ "The fisher exact test compute the probability p to randomly get the given set of value. \n" +
+ "This version compute the probability to get at least the given overlap between the given set and the given modality :\n" +
+ "Sum the hypergeometric probability with increasing target/query intersection cardinality.\n\n" +
+ "The hypergeometric probability is computed from the following contingency table entries.\n" +
+ "(value in cells correspond to the marginal totals of each intersection groups)\n" +
+ "\t\t\t\tQuery\t!Query\n" +
+ "\tTarget\t\ta\t\tb\n" +
+ "\t!Target\t\tc\t\td\n" +
+ "\n" +
+ "The probability of obtaining the set of value is computed as following:\n" +
+ "p = ((a+b)!(c+d)!(a+c)!(b+d)!)/(a!b!c!d!(a+b+c+d)!)\n" +
+ "\n" +
+ "The obtained p-value is then adjusted for multiple testing using one of the following methods:\n" +
+ " - Bonferroni: adjusted p-value = p*n\n" +
+ " - Benjamini-Hochberg: adjusted p-value = p*n/k\n" +
+ " - Holm-Bonferroni: adjusted p-value = p*(n+1-k)\n" +
+ "n : number of tests; k : pvalue rank";
+ }
+}