diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/BipartiteDistanceMatrix.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/BipartiteDistanceMatrix.java
new file mode 100644
index 0000000000000000000000000000000000000000..dc267e1f87a1e1e7e6577c6c424958c659de0317
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/BipartiteDistanceMatrix.java
@@ -0,0 +1,224 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+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.BioReaction;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.ShortestPath;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.UnweightedPolicy;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.WeightsFromFile;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.bipartite.BipartiteEdge;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.bipartite.BipartiteGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.io.Bionetwork2BioGraph;
+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_mapping.Mapper;
+import fr.inrae.toulouse.metexplore.met4j_mathUtils.matrix.BioMatrix;
+import fr.inrae.toulouse.metexplore.met4j_mathUtils.matrix.ExportMatrix;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.*;
+import org.kohsuke.args4j.Option;
+
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.stream.Stream;
+
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Csv;
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Sbml;
+import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumParameterTypes.*;
+
+public class BipartiteDistanceMatrix extends AbstractMet4jApplication {
+
+ @Format(name = Sbml)
+ @ParameterType(name = InputFile)
+ @Option(name = "-i", usage = "input SBML file", required = true)
+ public String inputPath = null;
+
+ @Format(name = Csv)
+ @ParameterType(name = OutputFile)
+ @Option(name = "-o", usage = "output Matrix file", required = true)
+ public String outputPath = null;
+
+ @Format(name = EnumFormats.Txt)
+ @ParameterType(name = InputFile)
+ @Option(name = "-sc", aliases = {"--side"}, usage = "an optional file containing list of side compounds to ignore")
+ public String sideCompoundFile = null;
+
+ @Format(name = EnumFormats.Txt)
+ @ParameterType(name = InputFile)
+ @Option(name = "-re", aliases = {"--rExclude"}, usage = "an optional file containing list of reactions to ignore")
+ public String rExclude = null;
+
+ @Format(name = EnumFormats.Txt)
+ @ParameterType(name = InputFile)
+ @Option(name = "-m", aliases = {"--mets"}, usage = "an optional file containing list of compounds of interest.")
+ public String metFile = null;
+
+ @Format(name = EnumFormats.Txt)
+ @ParameterType(name = InputFile)
+ @Option(name = "-r", aliases = {"--rxns"}, usage = "an optional file containing list of reactions of interest.")
+ public String rxnFile = null;
+
+ @Format(name = EnumFormats.Tsv)
+ @ParameterType(name = InputFile)
+ @Option(name = "-w", aliases = {"--weights"}, usage = "an optional file containing weights for compound pairs", forbids = {"-d"})
+ public String weightFile = null;
+
+ @Option(name = "-u", aliases = {"--undirected"}, usage = "Ignore reaction direction")
+ public Boolean undirected = false;
+
+ @Option(name = "-f", aliases = {"--full"}, usage = "compute full pairwise matrix from both reactions and compounds lists")
+ public Boolean full = false;
+
+
+ public static void main(String[] args) {
+
+ BipartiteDistanceMatrix app = new BipartiteDistanceMatrix();
+
+ app.parseArguments(args);
+
+ app.run();
+
+ }
+
+
+ public void run() {
+ //import network
+ JsbmlReader reader = new JsbmlReader(this.inputPath);
+
+ BioNetwork network = null;
+ try {
+ network = reader.read();
+ } catch (Met4jSbmlReaderException e) {
+ System.err.println("Error while reading the SBML file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+
+ //Create bipartite graph
+ Bionetwork2BioGraph builder = new Bionetwork2BioGraph(network);
+ BipartiteGraph graph = builder.getBipartiteGraph();
+
+ //Instantiate nodes to remove and mappers
+ Set<BioEntity> removedNodes = new HashSet<>();
+ Mapper<BioMetabolite> metMapper = new Mapper<>(network, BioNetwork::getMetabolitesView).skipIfNotFound();
+ Mapper<BioReaction> rxnMapper = new Mapper<>(network, BioNetwork::getReactionsView).skipIfNotFound();
+
+ //Graph processing: side compound removal [optional]
+ if (sideCompoundFile != null) {
+ System.err.println("removing side compounds...");
+ BioCollection<BioMetabolite> sideCpds = null;
+ try {
+ sideCpds = metMapper.map(sideCompoundFile);
+ } catch (IOException e) {
+ System.err.println("Error while reading the side compound file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ boolean removed = graph.removeAllVertices(sideCpds);
+ if(removed) removedNodes.addAll(sideCpds);
+ if (metMapper.getNumberOfSkippedEntries() > 0)
+ System.err.println(metMapper.getNumberOfSkippedEntries() + " side compounds not found in network.");
+ System.err.println(sideCpds.size() + " side compounds ignored during graph build.");
+ }
+
+ //Graph processing: reactions removal [optional]
+ if (rExclude != null) {
+ System.err.println("removing reactions to exclude...");
+ BioCollection<BioReaction> rList = null;
+ try {
+ rList = rxnMapper.map(rExclude);
+ } catch (IOException e) {
+ System.err.println("Error while reading the reaction to ignore file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ boolean removed = graph.removeAllVertices(rList);
+ if(removed) removedNodes.addAll(rList);
+ if (rxnMapper.getNumberOfSkippedEntries() > 0)
+ System.err.println(rxnMapper.getNumberOfSkippedEntries() + " reactions to exclude not found in network.");
+ System.err.println(rList.size() + " reactions ignored during graph build.");
+ }
+
+ //Graph processing: set weights [optional]
+ WeightingPolicy wp = new UnweightedPolicy();
+ if (weightFile != null) {
+ wp = new WeightsFromFile(weightFile, true);
+ }
+ wp.setWeight(graph);
+
+ //init BioMatrix
+ BioMatrix distM = null;
+ Set<BioEntity> metSeeds = null;
+ Set<BioEntity> rxnSeeds = null;
+
+ //If both seed files are missing, then compute on complete graphs
+ //If metabolite's seed file is missing, use the list of all metabolites nodes
+ // If metabolites's reaction file is missing, use the list of all reactions nodes
+
+ //Note cannot use mapper because bionetwork is not updated
+ if(metFile == null){
+ metSeeds = new HashSet<BioEntity>(graph.compoundVertexSet());
+ }else{
+ try {
+ metSeeds = new HashSet<>(metMapper.map(metFile));
+ } catch (IOException e) {
+ System.err.println("Error while reading the metabolite seeds file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ }
+ if(rxnFile == null){
+ rxnSeeds = new HashSet<BioEntity>(graph.reactionVertexSet());
+ }else{
+ try {
+ rxnSeeds = new HashSet<>(rxnMapper.map(rxnFile));
+ } catch (IOException e) {
+ System.err.println("Error while reading the metabolite seeds file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ }
+ //full == square distance matrix of all pairwise comparisons between seeds
+ if(full){
+ rxnSeeds.addAll(metSeeds);
+ metSeeds.addAll(rxnSeeds);
+ }
+ //clean metabolites seeds
+ boolean removedMets = metSeeds.removeAll(removedNodes);
+ if(removedMets) System.err.println("One or more seed nodes removed due to being in the side compounds list");
+ //clean reactions seeds
+ boolean removedRxns = rxnSeeds.removeAll(removedNodes);
+ if(removedRxns) System.err.println("One or more seed nodes removed due to being in the reaction to exclude list");
+ //compute distance matrix
+ ShortestPath<BioEntity,BipartiteEdge,BipartiteGraph> matrixComputor = new ShortestPath<>(graph, !undirected);
+ distM = matrixComputor.getShortestPathDistanceMatrix(metSeeds,rxnSeeds);
+ //export results
+ ExportMatrix.toCSV(outputPath, distM);
+
+ }
+
+ @Override
+ public String getLabel() {
+ return this.getClass().getSimpleName();
+ }
+
+ @Override
+ public String getLongDescription() {
+ return this.getShortDescription() + "\n" +
+ "The distance between two nodes (metabolite or reaction) is computed as the length of the shortest path connecting the two in the bipartite graph, " +
+ "Bipartite graph are composed of two distinct sets of nodes and two nodes can be linked only if they are from distinct sets.\n" +
+ "Therefore a metabolite node can be linked to a reaction node if the metabolite is a substrate or product of the reaction.\n" +
+ "An optional custom edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path." +
+ "Custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.\n" +
+ "If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.";
+ }
+
+ @Override
+ public String getShortDescription() {
+ return "Create a compound to reactions distance matrix.";
+ }
+}
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DistanceMatrix.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DistanceMatrix.java
index a6d784fbfafb447045837dd53b3dc4372b55a3ee..20a38175a15464496b301a20205d5cf478b21838 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DistanceMatrix.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DistanceMatrix.java
@@ -3,22 +3,18 @@ package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
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.collection.BioCollection;
-// import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.FloydWarshall;
-// import fr.inrae.toulouse.metexplore.met4j_graph.computation.utils.ComputeAdjacencyMatrix;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.ShortestPath;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.CustomWeightPolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.UnweightedPolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.DegreeWeightPolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.WeightsFromFile;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.BioGraph;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.BioPath;
import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
import fr.inrae.toulouse.metexplore.met4j_graph.io.Bionetwork2BioGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.io.NodeMapping;
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_mapping.Mapper;
import fr.inrae.toulouse.metexplore.met4j_mathUtils.matrix.BioMatrix;
import fr.inrae.toulouse.metexplore.met4j_mathUtils.matrix.ExportMatrix;
import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
@@ -27,7 +23,6 @@ import org.kohsuke.args4j.Option;
import java.io.IOException;
import java.util.LinkedHashSet;
-import java.util.List;
import java.util.Set;
import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Csv;
@@ -99,7 +94,7 @@ public class DistanceMatrix extends AbstractMet4jApplication {
//Graph processing: side compound removal [optional]
if (sideCompoundFile != null) {
System.err.println("removing side compounds...");
- Mapper<BioMetabolite> mapper = new Mapper<>(network, BioNetwork::getMetabolitesView).skipIfNotFound();
+ NodeMapping mapper = new NodeMapping<>(graph).skipIfNotFound();
BioCollection<BioMetabolite> sideCpds = null;
try {
sideCpds = mapper.map(sideCompoundFile);
@@ -108,10 +103,8 @@ public class DistanceMatrix extends AbstractMet4jApplication {
System.err.println(e.getMessage());
System.exit(1);
}
- if (mapper.getNumberOfSkippedEntries() > 0)
- System.err.println(mapper.getNumberOfSkippedEntries() + " side compounds not found in network.");
boolean removed = graph.removeAllVertices(sideCpds);
- System.err.println(sideCpds.size() + " side compounds ignored during graph build.");
+ if (removed) System.err.println(sideCpds.size() + " side compounds ignored during graph build.");
}
//Graph processing: set weights [optional]
@@ -148,7 +141,7 @@ public class DistanceMatrix extends AbstractMet4jApplication {
distM = matrixComputor.getShortestPathDistanceMatrix();
}else{
System.err.println("filtering matrix...");
- Mapper<BioMetabolite> mapper = new Mapper<>(network, BioNetwork::getMetabolitesView).skipIfNotFound();
+ NodeMapping mapper = new NodeMapping<>(graph).skipIfNotFound();
Set<BioMetabolite> seeds = null;
try {
seeds = new LinkedHashSet<BioMetabolite>(mapper.map(seedFile));
@@ -160,7 +153,6 @@ public class DistanceMatrix extends AbstractMet4jApplication {
//compute distance matrix
ShortestPath<BioMetabolite, ReactionEdge, CompoundGraph> matrixComputor = new ShortestPath<>(graph, !undirected);
//get SPs
- List<BioPath<BioMetabolite, ReactionEdge>> sps = matrixComputor.getShortestPathsUnionList(seeds);
distM = matrixComputor.getShortestPathDistanceMatrix(seeds,seeds);
}
//export results