From 80d0f20ecb29bcfdcb56005a25af2f0ef4b6b86e Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 1 Jun 2023 17:53:13 +0200
Subject: [PATCH 01/13] stub class for merging compartments
---
.../biodata/utils/CompartmentMerger.java | 169 ++++++++++++++++++
1 file changed, 169 insertions(+)
create mode 100644 met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
new file mode 100644
index 000000000..8adb1ac5e
--- /dev/null
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
@@ -0,0 +1,169 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.utils;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+
+import java.util.*;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+public class CompartmentMerger {
+
+ //criterion for identifying same compound over multiple compartments
+ //default use name as common field
+ Function<BioMetabolite,String> groupingFunction = BioMetabolite::getName;
+ //criterion for selecting a unique representative from a group of compound instances
+ //default takes first id in alphabetical order
+ Function<List<BioMetabolite>,BioMetabolite> pickFunction = (l -> {l.sort(Comparator.comparing(BioMetabolite::getId));return l.get(0);});
+ //unique compartment
+ //default is named "NA"
+ BioCompartment uniqComp = new BioCompartment("1", "NA");
+
+ // map for each compound toward their unique counterpart (can be themselves)
+ HashMap<BioMetabolite,BioMetabolite> convert;
+ // merged bioNetwork
+ BioNetwork merged;
+
+ public CompartmentMerger(){
+ }
+
+ public BioNetwork merge(BioNetwork original){
+
+ //create new network with same metadata and single compartment
+ buildNetwork(original);
+
+ //group corresponding compounds
+ Map<String, List<BioMetabolite>> compoundGroups = original.getMetabolitesView().stream().collect(Collectors.groupingBy(groupingFunction));
+
+ //for each group, create a unique compound
+ convert = new HashMap<>();
+ for(List<BioMetabolite> toContract : compoundGroups.values()){
+ BioMetabolite uniq = buildCompound(toContract); //(add newly created compound to new network)
+ //populate map for each compound toward their unique counterpart (can be themselves)
+ for(BioMetabolite m : toContract){
+ convert.put(m,uniq);
+ }
+ }
+
+ //copy Gene, Protein and Enzyme
+ keepGPR(original);
+
+ //for each reaction, replace reactants by their unique counterpart
+ for(BioReaction r : original.getReactionsView()){
+ // create deep copy, except for reactants
+ buildReaction(r);
+ }
+
+ //remove reactions that create loops
+ removeLoops();
+
+ //remove redundant reactions?
+ //TODO
+
+ //copy Pathways
+ //TODO
+
+ return merged;
+ }
+
+ private void buildNetwork(BioNetwork original){
+ //create new network with single compartment
+ merged = new BioNetwork();
+ merged.addCompartment(uniqComp);
+ //update metadata
+ merged.setSynonyms(new ArrayList<>(original.getSynonyms()));
+ merged.setComment(original.getComment());
+ merged.setRefs(new HashMap<>(original.getRefs()));
+ merged.setAttributes(new HashMap<>(original.getAttributes()));
+ }
+
+ private BioMetabolite buildCompound(List<BioMetabolite> originalCtoMerge){
+ //from compounds to merge, pick one as template for new unique compound
+ BioMetabolite chosen = pickFunction.apply(originalCtoMerge);
+ BioMetabolite newMetabolite = new BioMetabolite(chosen);
+ merged.add(newMetabolite);
+ merged.affectToCompartment(uniqComp,newMetabolite);
+ return newMetabolite;
+ }
+
+ private BioReaction buildReaction(BioReaction originalR){
+ BioReaction newReaction = new BioReaction(originalR);
+ newReaction.setSpontaneous(originalR.isSpontaneous());
+ newReaction.setReversible(originalR.isReversible());
+ newReaction.setEcNumber(originalR.getEcNumber());
+
+ merged.add(newReaction);
+
+ // Create substrates, swap to unique compound
+ for (BioReactant reactant : originalR.getLeftReactantsView()) {
+ BioMetabolite newMetabolite = convert.get(reactant.getMetabolite());
+ Double sto = reactant.getQuantity();
+ merged.affectLeft(newReaction, sto, uniqComp, newMetabolite);
+ }
+
+ // Create products, swap to unique compound
+ for (BioReactant reactant : originalR.getRightReactantsView()) {
+ BioMetabolite newMetabolite = convert.get(reactant.getMetabolite());
+ Double sto = reactant.getQuantity();
+ merged.affectRight(newReaction, sto, uniqComp, newMetabolite);
+ }
+
+ //copy GPR
+ for (BioEnzyme enzyme : originalR.getEnzymesView()) {
+ BioEnzyme newEnzyme = merged.getEnzyme(enzyme.getId());
+ merged.affectEnzyme(newReaction, newEnzyme);
+ }
+
+ return newReaction;
+ }
+
+ // remove reactions that create loops, i.e. transport reactions between compartments
+ private void removeLoops(){
+ BioCollection<BioReaction> toRemove = new BioCollection<>();
+ for(BioReaction r : merged.getReactionsView()){
+ if(r.getLeftsView().stream().anyMatch(r.getRightsView()::contains)) toRemove.add(r);
+ }
+ merged.removeOnCascade(toRemove);
+ }
+
+ private void keepGPR(BioNetwork original){
+ // Copy genes
+ for (BioGene gene : original.getGenesView()) {
+ BioGene newGene = new BioGene(gene);
+ merged.add(newGene);
+ }
+
+ // Copy proteins
+ for (BioProtein protein : original.getProteinsView()) {
+ BioProtein newProtein = new BioProtein(protein);
+ merged.add(newProtein);
+ if (protein.getGene() != null) {
+ String geneId = protein.getGene().getId();
+ BioGene newGene = merged.getGene(geneId);
+ merged.affectGeneProduct(newProtein, newGene);
+ }
+ }
+
+ // Copy enzymes
+ for (BioEnzyme enzyme : original.getEnzymesView()) {
+ BioEnzyme newEnzyme = new BioEnzyme(enzyme);
+ merged.add(newEnzyme);
+
+ BioCollection<BioEnzymeParticipant> participants = enzyme.getParticipantsView();
+
+ for (BioEnzymeParticipant participant : participants) {
+ Double quantity = participant.getQuantity();
+ if (participant.getPhysicalEntity().getClass().equals(BioMetabolite.class)) {
+ BioMetabolite metabolite = (BioMetabolite) participant.getPhysicalEntity();
+ // swap to unique compound
+ merged.affectSubUnit(newEnzyme, quantity, convert.get(metabolite));
+ } else if (participant.getPhysicalEntity().getClass().equals(BioProtein.class)) {
+ BioProtein protein = (BioProtein) participant.getPhysicalEntity();
+ BioProtein newProtein = merged.getProtein(protein.getId());
+ merged.affectSubUnit(newEnzyme, quantity, newProtein);
+ }
+ }
+ }
+ }
+
+}
--
GitLab
From 481d009cce89e861fd1bf171ea3a47eac668c791 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Mon, 5 Jun 2023 09:39:21 +0200
Subject: [PATCH 02/13] add options for merge functions, handle new compound id
collision, copy pathways
---
.../biodata/utils/CompartmentMerger.java | 46 +++++++++++++++++--
1 file changed, 41 insertions(+), 5 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
index 8adb1ac5e..4382f0e8d 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
@@ -11,10 +11,11 @@ public class CompartmentMerger {
//criterion for identifying same compound over multiple compartments
//default use name as common field
- Function<BioMetabolite,String> groupingFunction = BioMetabolite::getName;
+ Function<BioMetabolite,String> getUniqIdFunction = BioMetabolite::getName;
//criterion for selecting a unique representative from a group of compound instances
//default takes first id in alphabetical order
Function<List<BioMetabolite>,BioMetabolite> pickFunction = (l -> {l.sort(Comparator.comparing(BioMetabolite::getId));return l.get(0);});
+
//unique compartment
//default is named "NA"
BioCompartment uniqComp = new BioCompartment("1", "NA");
@@ -27,13 +28,28 @@ public class CompartmentMerger {
public CompartmentMerger(){
}
+ public CompartmentMerger setGetUniqIdFunction(Function<BioMetabolite, String> uniqIdFunction) {
+ this.getUniqIdFunction = uniqIdFunction;
+ return this;
+ }
+
+ public CompartmentMerger setCompoundMergeFunction(Function<List<BioMetabolite>, BioMetabolite> compoundMergeFunction) {
+ this.pickFunction = compoundMergeFunction;
+ return this;
+ }
+
+ public CompartmentMerger setUniqCompartment(BioCompartment uniqComp) {
+ this.uniqComp = uniqComp;
+ return this;
+ }
+
public BioNetwork merge(BioNetwork original){
//create new network with same metadata and single compartment
buildNetwork(original);
//group corresponding compounds
- Map<String, List<BioMetabolite>> compoundGroups = original.getMetabolitesView().stream().collect(Collectors.groupingBy(groupingFunction));
+ Map<String, List<BioMetabolite>> compoundGroups = original.getMetabolitesView().stream().collect(Collectors.groupingBy(getUniqIdFunction));
//for each group, create a unique compound
convert = new HashMap<>();
@@ -54,15 +70,27 @@ public class CompartmentMerger {
buildReaction(r);
}
+ //copy Pathways
+ for (BioPathway pathway : original.getPathwaysView()) {
+
+ BioPathway newPathway = new BioPathway(pathway);
+ merged.add(newPathway);
+
+ // Add reactions into pathway
+ BioCollection<BioReaction> reactions = original.getReactionsFromPathways(pathway);
+
+ for (BioReaction reaction : reactions) {
+ BioReaction newReaction = merged.getReaction(reaction.getId());
+ merged.affectToPathway(newPathway, newReaction);
+ }
+ }
+
//remove reactions that create loops
removeLoops();
//remove redundant reactions?
//TODO
- //copy Pathways
- //TODO
-
return merged;
}
@@ -81,6 +109,14 @@ public class CompartmentMerger {
//from compounds to merge, pick one as template for new unique compound
BioMetabolite chosen = pickFunction.apply(originalCtoMerge);
BioMetabolite newMetabolite = new BioMetabolite(chosen);
+ BioMetabolite old = merged.getMetabolite(newMetabolite.getId());
+ if(old!=null){
+ System.err.println("WARNING: collision in new compound identifiers. Compounds with different unique ids will be merged under the same new entity "+newMetabolite.getId()+".");
+ System.err.println("If it is an expected behaviour that the provided merge function may not produce a different compounds at each call, please review the following merge:");
+ System.err.println(originalCtoMerge.stream().map(c -> c.getId()+" : "+ getUniqIdFunction.apply(c)).collect(Collectors.toList()));
+ System.err.println(convert.entrySet().stream().filter(e -> old.equals(e.getValue())).map(e -> e.getKey().getId()+" : "+ getUniqIdFunction.apply(e.getKey())).collect(Collectors.toList()));
+ return old;
+ }
merged.add(newMetabolite);
merged.affectToCompartment(uniqComp,newMetabolite);
return newMetabolite;
--
GitLab
From ed40b6ebbdc996692468ea773005769cfe3aa518 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 8 Jun 2023 16:11:59 +0200
Subject: [PATCH 03/13] add javadoc
---
.../biodata/utils/CompartmentMerger.java | 32 +++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
index 4382f0e8d..523a50652 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
@@ -7,6 +7,9 @@ import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
+/**
+ * A class to create, from a network with multiple compartments, a new network with a single compartment, avoiding duplicated compounds.
+ */
public class CompartmentMerger {
//criterion for identifying same compound over multiple compartments
@@ -25,24 +28,52 @@ public class CompartmentMerger {
// merged bioNetwork
BioNetwork merged;
+ /**
+ * Create a new Compartment Merger
+ */
public CompartmentMerger(){
}
+ /**
+ * Fluent builder setting the function that provides the criterion used for identifying same compounds over multiple compartments
+ * Default use "name" as common field for the same compound over multiple compartments
+ * @param uniqIdFunction the function
+ * @return a CompartmentMerger instance
+ */
public CompartmentMerger setGetUniqIdFunction(Function<BioMetabolite, String> uniqIdFunction) {
this.getUniqIdFunction = uniqIdFunction;
return this;
}
+ /**
+ * Fluent builder setting the function that select or create a unique representative from a group of compound instances
+ * default return compound from list with first id in alphabetical order.
+ * A new compound with custom id can be returned, but if an id is generated twice or more, the corresponding groups will be merged into a single one
+ * @param compoundMergeFunction the function
+ * @return a CompartmentMerger instance
+ */
public CompartmentMerger setCompoundMergeFunction(Function<List<BioMetabolite>, BioMetabolite> compoundMergeFunction) {
this.pickFunction = compoundMergeFunction;
return this;
}
+ /**
+ * Fluent builder setting the compartment where all the compounds will be merged.
+ * Default is a compartment named "NA".
+ * @param uniqComp the single compartment
+ * @return a CompartmentMerger instance
+ */
public CompartmentMerger setUniqCompartment(BioCompartment uniqComp) {
this.uniqComp = uniqComp;
return this;
}
+ /**
+ * Merge compartments by indexing compounds to identify groups of same compounds over different compartments, and select or
+ * create a unique compound to be added to a new single compartment.
+ * @param original the original network
+ * @return a network with merged compartments
+ */
public BioNetwork merge(BioNetwork original){
//create new network with same metadata and single compartment
@@ -162,6 +193,7 @@ public class CompartmentMerger {
merged.removeOnCascade(toRemove);
}
+ // copy Gene, Protein and Enzyme from original network
private void keepGPR(BioNetwork original){
// Copy genes
for (BioGene gene : original.getGenesView()) {
--
GitLab
From d37f1082f04bfcef7e84d4dd7599b66bf77e2a5f Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Wed, 14 Jun 2023 16:56:57 +0200
Subject: [PATCH 04/13] option to set new network name
---
.../biodata/utils/CompartmentMerger.java | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
index 523a50652..c661c21cb 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
@@ -28,6 +28,9 @@ public class CompartmentMerger {
// merged bioNetwork
BioNetwork merged;
+ // merged network name
+ String name;
+
/**
* Create a new Compartment Merger
*/
@@ -68,6 +71,17 @@ public class CompartmentMerger {
return this;
}
+ /**
+ * Fluent builder setting the merged network name.
+ * Default append "_compartments-merged" to original network name.
+ * @param name the name
+ * @return a CompartmentMerger instance
+ */
+ public CompartmentMerger setNewNetworkName(String name) {
+ this.name = name;
+ return this;
+ }
+
/**
* Merge compartments by indexing compounds to identify groups of same compounds over different compartments, and select or
* create a unique compound to be added to a new single compartment.
@@ -128,6 +142,11 @@ public class CompartmentMerger {
private void buildNetwork(BioNetwork original){
//create new network with single compartment
merged = new BioNetwork();
+ if(name == null){
+ merged.setName(original.getName()+"_compartments-merged");
+ }else{
+ merged.setName(name);
+ }
merged.addCompartment(uniqComp);
//update metadata
merged.setSynonyms(new ArrayList<>(original.getSynonyms()));
--
GitLab
From 09d9b34b45a8ff6be0ea0c9e1d489325f8b4984d Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Wed, 14 Jun 2023 16:57:35 +0200
Subject: [PATCH 05/13] [Toolbox][convert] new app to process sbml, including
compartment merging
---
.../met4j_toolbox/convert/ProcessSBML.java | 221 ++++++++++++++++++
1 file changed, 221 insertions(+)
create mode 100644 met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
new file mode 100644
index 000000000..897bfcfab
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
@@ -0,0 +1,221 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.convert;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.utils.CompartmentMerger;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.*;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.EdgeMerger;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.VertexContraction;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.utils.ComputeAdjacencyMatrix;
+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.ExportGraph;
+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_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_io.jsbml.writer.JsbmlWriter;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.Met4jSbmlWriterException;
+import fr.inrae.toulouse.metexplore.met4j_mapping.Mapper;
+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.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 fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis.CompoundNet;
+import org.kohsuke.args4j.Option;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+
+public class ProcessSBML extends AbstractMet4jApplication {
+
+ @Format(name = EnumFormats.Sbml)
+ @ParameterType(name = EnumParameterTypes.InputFile)
+ @Option(name = "-s", usage = "input SBML file", required = true)
+ public String inputPath = null;
+
+ @ParameterType(name = EnumParameterTypes.InputFile)
+ @Format(name = EnumFormats.Txt)
+ @Option(name = "-rc", usage = "remove compounds from input identifier file", required = false)
+ public String inputSide = null;
+
+ @ParameterType(name = EnumParameterTypes.InputFile)
+ @Format(name = EnumFormats.Txt)
+ @Option(name = "-rr", usage = "remove reaction from input identifier file", required = false)
+ public String inputReactions = null;
+
+ @ParameterType(name = EnumParameterTypes.OutputFile)
+ @Format(name = EnumFormats.Sbml)
+ @Option(name = "-o", usage = "output SBML file", required = true)
+ public String outputPath = null;
+
+ enum strategy {no, by_name, by_id}
+
+ @Option(name = "-mc", aliases = {"--mergecomp"}, usage = "merge compartments. " +
+ "Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form \"xxx_y\" with xxx as base identifier and y as compartment label).")
+ public strategy mergingStrat = strategy.no;
+ public String idRegex = "^(\\w+)_\\w$";
+
+
+ @Option(name = "-rEX", aliases = {"--removeExchange"}, usage = "remove exchange reactions and species from given exchange compartment identifier", required = false)
+ public String exchangeCompToRemove;
+
+ public static void main(String[] args) throws Met4jSbmlWriterException, IOException {
+
+ ProcessSBML app = new ProcessSBML();
+
+ app.parseArguments(args);
+
+ app.run();
+
+ }
+
+
+ public void run() throws Met4jSbmlWriterException, IOException {
+ System.out.print("Reading SBML...");
+ JsbmlReader reader = new JsbmlReader(this.inputPath);
+ 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.");
+
+ //print info
+ System.out.println("\tcompartments:\t"+network.getCompartmentsView().size());
+ System.out.println("\tmetabolites:\t"+network.getMetabolitesView().size());
+ System.out.println("\treactions:\t"+network.getReactionsView().size());
+ System.out.println("\tenzymes:\t"+network.getEnzymesView().size());
+ System.out.println("\tgenes:\t"+network.getGenesView().size());
+ System.out.println("\tprotein:\t"+network.getProteinsView().size());
+ System.out.println("\tpathway:\t"+network.getPathwaysView().size());
+
+ //side compound removal [optional]
+ if (inputSide != null) {
+ BioCollection<BioMetabolite> sideCpds = new BioCollection<>();
+ System.err.println("removing side compounds...");
+ Mapper<BioMetabolite> cmapper = new Mapper<>(network, BioNetwork::getMetabolitesView).skipIfNotFound();
+
+ try {
+ sideCpds = cmapper.map(inputSide);
+ } catch (IOException e) {
+ System.err.println("Error while reading the side compound file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ if (cmapper.getNumberOfSkippedEntries() > 0)
+ System.err.println(cmapper.getNumberOfSkippedEntries() + " side compounds not found in network.");
+
+ for(BioMetabolite sc : sideCpds){
+ network.removeOnCascade(sc);
+ }
+ System.err.println(sideCpds.size() + " side compounds removed from network.");
+ }
+
+ //irrelevant reaction removal [optional]
+ if (inputReactions != null) {
+ BioCollection<BioReaction> sideRxns = new BioCollection<>();
+ System.err.println("removing side reaction...");
+ Mapper<BioReaction> rmapper = new Mapper<>(network, BioNetwork::getReactionsView).skipIfNotFound();
+
+ try {
+ sideRxns = rmapper.map(inputReactions);
+ } catch (IOException e) {
+ System.err.println("Error while reading the irrelevant reactions file");
+ System.err.println(e.getMessage());
+ System.exit(1);
+ }
+ if (rmapper.getNumberOfSkippedEntries() > 0)
+ System.err.println(rmapper.getNumberOfSkippedEntries() + " reactions not found in network.");
+
+ for(BioReaction r : sideRxns){
+ network.removeOnCascade(r);
+ }
+ System.err.println(sideRxns.size() + " irrelevant reactions removed from network.");
+ }
+
+ //exchange reaction removal
+ if(exchangeCompToRemove!=null){
+ System.err.println("removing external compartment...");
+ BioCompartment exchange = network.getCompartment(exchangeCompToRemove);
+ if(exchange==null){
+ System.err.println("Exchange compartment not found, please check provided identifier");
+ }else{
+ int n = 0;
+ for (BioEntity e : exchange.getComponentsView()){
+ network.removeOnCascade(e);
+ n++;
+ }
+ System.err.println(n + " external species removed from network.");
+ }
+ }
+
+ //merge compartment
+ BioNetwork newNetwork;
+ if (mergingStrat == strategy.by_id) {
+ System.err.print("Merging compartments...");
+ CompartmentMerger merger = new CompartmentMerger()
+ .setGetUniqIdFunction(c -> c.getId().substring(0,c.getId().length()-2))
+ .setCompoundMergeFunction((l -> {
+ BioMetabolite oldComp = l.get(0);
+ return new BioMetabolite(oldComp,oldComp.getId().substring(0,oldComp.getId().length()-2));
+ }));
+ newNetwork = merger.merge(network);
+ System.err.println(" Done.");
+ }else if (mergingStrat != strategy.by_name) {
+ System.err.print("Merging compartments...");
+ CompartmentMerger merger = new CompartmentMerger()
+ .setGetUniqIdFunction(BioMetabolite::getName);
+ newNetwork = merger.merge(network);
+ System.err.println(" Done.");
+ }else{
+ newNetwork = network;
+ }
+
+ //print info
+ System.out.println("\tcompartments:\t"+newNetwork.getCompartmentsView().size());
+ System.out.println("\tmetabolites:\t"+newNetwork.getMetabolitesView().size());
+ System.out.println("\treactions:\t"+newNetwork.getReactionsView().size());
+ System.out.println("\tenzymes:\t"+newNetwork.getEnzymesView().size());
+ System.out.println("\tgenes:\t"+newNetwork.getGenesView().size());
+ System.out.println("\tprotein:\t"+newNetwork.getProteinsView().size());
+ System.out.println("\tpathway:\t"+newNetwork.getPathwaysView().size());
+
+ //export network
+ System.out.print("Exporting...");
+ new JsbmlWriter(outputPath,newNetwork).write();
+ System.out.println(" Done.");
+ return;
+ }
+
+ @Override
+ public String getLabel() {
+ return this.getClass().getSimpleName();
+ }
+
+ @Override
+ public String getLongDescription() {
+ return "General SBML model processing including compound removal (such as side compounds), reaction removal (blocked or exchange reaction), and compartments merging";
+ }
+
+ @Override
+ public String getShortDescription() {
+ return "General SBML model processing";
+ }
+}
--
GitLab
From 7252b2ff1e29b7738792360bd33fa064e8c82256 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 15 Jun 2023 17:11:05 +0200
Subject: [PATCH 06/13] add option to remove reaction with closed flux bounds
---
.../met4j_toolbox/convert/ProcessSBML.java | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
index 897bfcfab..fbe114e50 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
@@ -13,6 +13,7 @@ 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.ExportGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.io.NodeMapping;
+import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.ReactionAttributes;
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;
@@ -58,6 +59,9 @@ public class ProcessSBML extends AbstractMet4jApplication {
@Option(name = "-o", usage = "output SBML file", required = true)
public String outputPath = null;
+ @Option(name = "-r0", aliases = {"--noFlux"}, usage = "remove reactions with lower and upper flux bounds both set to 0.0")
+ public boolean removeNoFlux;
+
enum strategy {no, by_name, by_id}
@Option(name = "-mc", aliases = {"--mergecomp"}, usage = "merge compartments. " +
@@ -150,6 +154,21 @@ public class ProcessSBML extends AbstractMet4jApplication {
System.err.println(sideRxns.size() + " irrelevant reactions removed from network.");
}
+ //removal of reactions that cannot hold flux in any condition
+ if(removeNoFlux){
+ System.err.println("removing reaction with closed flux bound...");
+ BioCollection<BioReaction> toRemove = new BioCollection<>();
+ for(BioReaction r : network.getReactionsView()){
+ if(ReactionAttributes.getLowerBound(r).value==0.0 &&
+ ReactionAttributes.getUpperBound(r).value==0.0){
+ toRemove.add(r);
+ }
+ }
+
+ network.removeOnCascade(toRemove);
+ System.err.println(toRemove.size() + " external species removed from network.");
+ }
+
//exchange reaction removal
if(exchangeCompToRemove!=null){
System.err.println("removing external compartment...");
--
GitLab
From ef443d4bbc1304403e1aa911bd1b5761282ed876 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Wed, 21 Jun 2023 16:38:28 +0200
Subject: [PATCH 07/13] add unit test
---
.../biodata/utils/CompartmentMergerTest.java | 129 ++++++++++++++++++
1 file changed, 129 insertions(+)
create mode 100644 met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
new file mode 100644
index 000000000..510e32539
--- /dev/null
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
@@ -0,0 +1,129 @@
+package fr.inrae.toulouse.metexplore.met4j_core.biodata.utils;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class CompartmentMergerTest {
+
+
+ BioNetwork network;
+ BioReaction r1,r2,r1X,r3,rt1,rt2;
+ BioMetabolite a,b,c,d,aX,bX,cX,eX;
+ BioCompartment comp0,compX,compMerge;
+ BioProtein p1;
+ BioGene g1;
+ BioEnzyme e1;
+
+ @Before
+ public void init() {
+ network = new BioNetwork();
+ r1 = new BioReaction("r1");
+ r2 = new BioReaction("r2");
+ r1X = new BioReaction("r1X");
+ r3 = new BioReaction("r3");
+ rt1 = new BioReaction("rt1");
+ rt2 = new BioReaction("rt2");
+ network.add(r1,r2,r1X,r3,rt1,rt2);
+
+ a = new BioMetabolite("a_0", "a");
+ b = new BioMetabolite("b_0", "b");
+ c = new BioMetabolite("c_0", "c");
+ d = new BioMetabolite("d_0", "d");
+ aX = new BioMetabolite("a_X", "a");
+ bX = new BioMetabolite("b_X", "b");
+ cX = new BioMetabolite("c_X", "c");
+ eX = new BioMetabolite("d_X", "e");
+ network.add(a,b,c,d,aX,bX,cX,eX);
+ comp0 = new BioCompartment("0");
+ compX = new BioCompartment("X");
+ compMerge = new BioCompartment("merge");
+ network.add(comp0,compX);
+ network.affectToCompartment(comp0, a, b, c, d);
+ network.affectToCompartment(compX, aX, bX, cX, eX);
+
+ network.affectLeft(r1, 2.0, comp0, a);
+ network.affectRight(r1, 1.0, comp0, b);
+ network.affectRight(r1, 1.0, comp0, c);
+ r1.setReversible(false);
+
+ network.affectLeft(r1X, 2.0, compX, aX);
+ network.affectRight(r1X, 1.0, compX, bX);
+ network.affectRight(r1X, 1.0, compX, cX);
+ r1X.setReversible(false);
+
+ network.affectLeft(r2, 1.0, comp0, c);
+ network.affectRight(r2, 1.0, comp0, d);
+ r2.setReversible(false);
+
+ network.affectLeft(r3, 1.0, compX, cX);
+ network.affectRight(r3, 1.0, compX, eX);
+ r3.setReversible(false);
+
+ network.affectLeft(rt1, 1.0, comp0, a);
+ network.affectRight(rt1, 1.0, compX, aX);
+ rt1.setReversible(true);
+
+ network.affectLeft(rt2, 1.0, comp0, c);
+ network.affectRight(rt2, 1.0, compX, cX);
+ rt2.setReversible(true);
+
+
+ e1 = new BioEnzyme("e1");
+ network.add(e1);
+ p1 = new BioProtein("p1");
+ network.add(p1);
+ g1 = new BioGene("g1", "G1");
+ network.add(g1);
+ network.affectGeneProduct(p1, g1);
+ network.affectSubUnit(e1, 1.0, p1);
+ network.affectEnzyme(r3, e1);
+
+ }
+
+ @Test
+ public void testMerge() {
+ CompartmentMerger merger = new CompartmentMerger()
+ .setNewNetworkName("myNewName")
+ .setUniqCompartment(compMerge)
+ .setGetUniqIdFunction(BioMetabolite::getName);
+
+ BioNetwork newNetwork = merger.merge(network);
+ assertEquals("Error while setting new name","myNewName",newNetwork.getName());
+ assertTrue("Error while creating new compartment",newNetwork.containsCompartment("merge"));
+ assertEquals("Error while merging compartment, wrong number of final compartments",1,newNetwork.getCompartmentsView().size());
+ assertEquals("Error while merging compartment, wrong number of final metabolites",5,newNetwork.getMetabolitesView().size());
+ assertEquals("Error while merging compartment, wrong number of final reactions",4,newNetwork.getReactionsView().size());
+ assertFalse("Error while merging compartment, gene lost",newNetwork.getGenesView().isEmpty());
+ assertFalse("Error while merging compartment, enzyme lost",newNetwork.getEnzymesView().isEmpty());
+ assertFalse("Error while merging compartment, protein lost",newNetwork.getProteinsView().isEmpty());
+ }
+
+ public void testMergeII() {
+ CompartmentMerger merger = new CompartmentMerger()
+ .setNewNetworkName("myNewName")
+ .setUniqCompartment(compMerge)
+ .setGetUniqIdFunction(c -> c.getId().substring(0,c.getId().length()-2))
+ .setCompoundMergeFunction((l -> {
+ BioMetabolite oldComp = l.get(0);
+ return new BioMetabolite(oldComp,oldComp.getId().substring(0,oldComp.getId().length()-2));
+ }));
+
+ BioNetwork newNetwork = merger.merge(network);
+ assertEquals("Error while setting new name","myNewName",newNetwork.getName());
+ assertTrue("Error while creating new compartment",newNetwork.containsCompartment("merge"));
+ assertEquals("Error while merging compartment, wrong number of final compartments",1,newNetwork.getCompartmentsView().size());
+ assertEquals("Error while merging compartment, wrong number of final metabolites",5,newNetwork.getMetabolitesView().size());
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("a"));
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("b"));
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("c"));
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("d"));
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("e"));
+ assertEquals("Error while merging compartment, wrong number of final reactions",4,newNetwork.getReactionsView().size());
+ assertFalse("Error while merging compartment, gene lost",newNetwork.getGenesView().isEmpty());
+ assertFalse("Error while merging compartment, enzyme lost",newNetwork.getEnzymesView().isEmpty());
+ assertFalse("Error while merging compartment, protein lost",newNetwork.getProteinsView().isEmpty());
+ }
+}
--
GitLab
From ea6b145e28167b963c907e54a98114362a680464 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Wed, 21 Jun 2023 17:31:55 +0200
Subject: [PATCH 08/13] add utilities for "by id" merging using palsson
convention or base-id extraction regex
---
.../biodata/utils/CompartmentMerger.java | 45 ++++++++++++++++++-
.../biodata/utils/CompartmentMergerTest.java | 28 +++++++++---
2 files changed, 67 insertions(+), 6 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
index c661c21cb..5a813f3c1 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMerger.java
@@ -5,6 +5,8 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
import java.util.*;
import java.util.function.Function;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import java.util.stream.Collectors;
/**
@@ -38,7 +40,8 @@ public class CompartmentMerger {
}
/**
- * Fluent builder setting the function that provides the criterion used for identifying same compounds over multiple compartments
+ * Fluent builder setting the function that provides the criterion used for identifying same compounds over multiple compartments,
+ * using a custom function provided as argument.
* Default use "name" as common field for the same compound over multiple compartments
* @param uniqIdFunction the function
* @return a CompartmentMerger instance
@@ -48,6 +51,46 @@ public class CompartmentMerger {
return this;
}
+ /**
+ * Fluent builder setting both functions that provides the criterion used for identifying same compounds over multiple compartments,
+ * and that creates a unique representative for such compounds, using a common identifier convention.
+ * This will strip the two last characters from compound identifiers to create shared ids that will be used in final merged network.
+ * This should be used for SBML that use the naming convention "xxx_y" for compounds, where xxx is the base identifier and y is the compound identifier (single letter).
+ * @return a CompartmentMerger instance
+ */
+ public CompartmentMerger usePalssonIdentifierConvention() {
+ this.getUniqIdFunction = c -> c.getId().substring(0,c.getId().length()-2);
+ this.pickFunction = (l -> {
+ BioMetabolite oldComp = l.get(0);
+ return new BioMetabolite(oldComp,oldComp.getId().substring(0,oldComp.getId().length()-2));
+ });
+ return this;
+ }
+
+ /**
+ * Fluent builder setting both functions that provides the criterion used for identifying same compounds over multiple compartments,
+ * and that creates a unique representative for such compounds, when compound identifiers contains explicit compartment info.
+ * This use a provided regex to extract a shared base identifier from compound identifiers, and used it in final merged network.
+ * This should be used for SBML that use a compound identifier convention containing a base identifier and a compartment suffix/prefix,
+ * such as "xxx_y" (regex "^(\\w+)_\\w$") "xxx[y]" or "xxx-yyy", where xxx is the base identifier and y is the compound identifier.
+ * @return a CompartmentMerger instance
+ */
+ public CompartmentMerger useBaseIdentifierRegex(String regex) {
+ this.getUniqIdFunction = (v ->{
+ String id = v.getId();
+ Matcher m = Pattern.compile(regex).matcher(id);
+ if(m.matches()) id=m.group(1);
+ return id;});
+ this.pickFunction = (l -> {
+ BioMetabolite oldComp = l.get(0);
+ String id = oldComp.getId();
+ Matcher m = Pattern.compile(regex).matcher(id);
+ if(m.matches()) id=m.group(1);
+ return new BioMetabolite(oldComp,id);
+ });
+ return this;
+ }
+
/**
* Fluent builder setting the function that select or create a unique representative from a group of compound instances
* default return compound from list with first id in alphabetical order.
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
index 510e32539..734d41c8e 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
@@ -105,11 +105,7 @@ public class CompartmentMergerTest {
CompartmentMerger merger = new CompartmentMerger()
.setNewNetworkName("myNewName")
.setUniqCompartment(compMerge)
- .setGetUniqIdFunction(c -> c.getId().substring(0,c.getId().length()-2))
- .setCompoundMergeFunction((l -> {
- BioMetabolite oldComp = l.get(0);
- return new BioMetabolite(oldComp,oldComp.getId().substring(0,oldComp.getId().length()-2));
- }));
+ .usePalssonIdentifierConvention();
BioNetwork newNetwork = merger.merge(network);
assertEquals("Error while setting new name","myNewName",newNetwork.getName());
@@ -126,4 +122,26 @@ public class CompartmentMergerTest {
assertFalse("Error while merging compartment, enzyme lost",newNetwork.getEnzymesView().isEmpty());
assertFalse("Error while merging compartment, protein lost",newNetwork.getProteinsView().isEmpty());
}
+
+ public void testMergeIII() {
+ CompartmentMerger merger = new CompartmentMerger()
+ .setNewNetworkName("myNewName")
+ .setUniqCompartment(compMerge)
+ .useBaseIdentifierRegex("^(\\w+)_\\w$");
+
+ BioNetwork newNetwork = merger.merge(network);
+ assertEquals("Error while setting new name","myNewName",newNetwork.getName());
+ assertTrue("Error while creating new compartment",newNetwork.containsCompartment("merge"));
+ assertEquals("Error while merging compartment, wrong number of final compartments",1,newNetwork.getCompartmentsView().size());
+ assertEquals("Error while merging compartment, wrong number of final metabolites",5,newNetwork.getMetabolitesView().size());
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("a"));
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("b"));
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("c"));
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("d"));
+ assertTrue("Error while merging compartment, wrong merged metabolite",newNetwork.containsMetabolite("e"));
+ assertEquals("Error while merging compartment, wrong number of final reactions",4,newNetwork.getReactionsView().size());
+ assertFalse("Error while merging compartment, gene lost",newNetwork.getGenesView().isEmpty());
+ assertFalse("Error while merging compartment, enzyme lost",newNetwork.getEnzymesView().isEmpty());
+ assertFalse("Error while merging compartment, protein lost",newNetwork.getProteinsView().isEmpty());
+ }
}
--
GitLab
From 0a171c65a0ef53e9b2e74c0288d05841dc7bf364 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Wed, 21 Jun 2023 18:46:49 +0200
Subject: [PATCH 09/13] fix tests
---
.../met4j_core/biodata/utils/CompartmentMergerTest.java | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
index 734d41c8e..6f31b2088 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/CompartmentMergerTest.java
@@ -35,7 +35,7 @@ public class CompartmentMergerTest {
aX = new BioMetabolite("a_X", "a");
bX = new BioMetabolite("b_X", "b");
cX = new BioMetabolite("c_X", "c");
- eX = new BioMetabolite("d_X", "e");
+ eX = new BioMetabolite("e_X", "e");
network.add(a,b,c,d,aX,bX,cX,eX);
comp0 = new BioCompartment("0");
compX = new BioCompartment("X");
@@ -85,6 +85,7 @@ public class CompartmentMergerTest {
@Test
public void testMerge() {
+ a.setName("a");
CompartmentMerger merger = new CompartmentMerger()
.setNewNetworkName("myNewName")
.setUniqCompartment(compMerge)
@@ -101,7 +102,9 @@ public class CompartmentMergerTest {
assertFalse("Error while merging compartment, protein lost",newNetwork.getProteinsView().isEmpty());
}
+ @Test
public void testMergeII() {
+ a.setName("notA");//break default merging strategy
CompartmentMerger merger = new CompartmentMerger()
.setNewNetworkName("myNewName")
.setUniqCompartment(compMerge)
@@ -123,7 +126,9 @@ public class CompartmentMergerTest {
assertFalse("Error while merging compartment, protein lost",newNetwork.getProteinsView().isEmpty());
}
+ @Test
public void testMergeIII() {
+ a.setName("notA");//break default merging strategy
CompartmentMerger merger = new CompartmentMerger()
.setNewNetworkName("myNewName")
.setUniqCompartment(compMerge)
@@ -144,4 +149,5 @@ public class CompartmentMergerTest {
assertFalse("Error while merging compartment, enzyme lost",newNetwork.getEnzymesView().isEmpty());
assertFalse("Error while merging compartment, protein lost",newNetwork.getProteinsView().isEmpty());
}
+
}
--
GitLab
From 967182cd6b6e2b2b17fe7ee492690e0e5091ef33 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 22 Jun 2023 11:59:56 +0200
Subject: [PATCH 10/13] add option to handle GPR in reaction redundance check +
add method for removal of all redundant reaction in BioNetworkUtils
---
.../biodata/utils/BioNetworkUtils.java | 21 +++++++++++
.../biodata/utils/BioReactionUtils.java | 28 +++++++++++----
.../biodata/utils/BioReactionUtilsTest.java | 35 +++++++++++++++++++
3 files changed, 78 insertions(+), 6 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
index 30d311a5e..bf66a9cbb 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
@@ -104,6 +104,27 @@ public class BioNetworkUtils {
}
}
+ /**
+ * Remove from a network all duplicated reactions
+ *
+ * @param network a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork}
+ * @param checkSameGPR if reactions should be considered non-redundant if they share same reactants but have different GPR
+ */
+ public static void removeDuplicatedReactions(@NonNull BioNetwork network, boolean checkSameGPR) {
+ ArrayList<BioReaction> reactions = new ArrayList<>(network.getReactionsView());
+ BioCollection<BioReaction> toRemove = new BioCollection<>();
+ for (int i = 0; i < reactions.size(); i++){
+ for (int j = i + 1; j < reactions.size(); j++) {
+ BioReaction r1 = reactions.get(i);
+ BioReaction r2 = reactions.get(j);
+ if(BioReactionUtils.areRedundant(network,r1,r2,checkSameGPR)){
+ toRemove.add(r1);
+ }
+ }
+ }
+ network.removeOnCascade(toRemove);
+ }
+
public static void deepCopy(BioNetwork networkIn, BioNetwork networkOut) {
deepCopy(networkIn, networkOut, true, false);
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioReactionUtils.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioReactionUtils.java
index 4dafe8eea..8f9921e72 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioReactionUtils.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioReactionUtils.java
@@ -59,10 +59,11 @@ public class BioReactionUtils {
* @param network a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork}
* @param r1 a first {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction}
* @param r2 a second {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction}
- * @return true if the substrates and the products have the same id
+ * @param checkSameGPR if reactions should be considered non-redundant if they share same reactants but have different GPR
+ * @return true if the two reactions are redundant (same reactants and optionally same GPR)
* @throws java.lang.IllegalArgumentException if one of the reaction is not in the network
*/
- public static Boolean areRedundant(@NonNull BioNetwork network, @NonNull BioReaction r1, @NonNull BioReaction r2) {
+ public static Boolean areRedundant(@NonNull BioNetwork network, @NonNull BioReaction r1, @NonNull BioReaction r2, boolean checkSameGPR) {
if (!network.contains(r1)) {
@@ -88,18 +89,33 @@ public class BioReactionUtils {
rightR1.containsAll(rightR2) &&
rightR2.containsAll(rightR1);
- if (!r1.isReversible()) {
- return flag1;
- } else {
+ if (r1.isReversible()) {
Boolean flag2 = rightR1.containsAll(leftR2) &&
leftR2.containsAll(rightR1) &&
leftR1.containsAll(rightR2) &&
rightR2.containsAll(leftR1);
- return flag1 || flag2;
+ flag1 = (flag1 || flag2);
+ }
+
+ if(flag1 && checkSameGPR){
+ return BioReactionUtils.getGPR(network, r1).equals(BioReactionUtils.getGPR(network, r2));
}
+ return flag1;
+ }
+ /**
+ * Comparison of two reactions
+ *
+ * @param network a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork}
+ * @param r1 a first {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction}
+ * @param r2 a second {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction}
+ * @return true if the substrates and the products have the same id
+ * @throws java.lang.IllegalArgumentException if one of the reaction is not in the network
+ */
+ public static Boolean areRedundant(@NonNull BioNetwork network, @NonNull BioReaction r1, @NonNull BioReaction r2) {
+ return areRedundant(network, r1, r2, false);
}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioReactionUtilsTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioReactionUtilsTest.java
index 92bd22a50..bd031882d 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioReactionUtilsTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioReactionUtilsTest.java
@@ -121,6 +121,41 @@ public class BioReactionUtilsTest {
}
+ /**
+ * Test method for
+ * {@link BioReactionUtils#areRedundant(BioNetwork, BioReaction, BioReaction)}.
+ */
+ @Test
+ public void testAreRedundantCheckGPR() {
+
+ BioReaction r2 = new BioReaction("r2");
+ r2.setReversible(false);
+ network.add(r2);
+
+ network.affectLeft(r2, 1.0, c, m1);
+ network.affectRight(r2, 2.0, c, m2);
+ network.affectRight(r2, 1.5, c, m3);
+
+ network.affectGeneProduct(p1, g1);
+ network.affectGeneProduct(p2, g1);
+ network.affectGeneProduct(p3, g1);
+
+ network.affectSubUnit(e1, 1.0, p1);
+ network.affectSubUnit(e1, 1.0, p2);
+ network.affectSubUnit(e2, 1.0, p3);
+
+ network.affectEnzyme(r1, e1);
+ network.affectEnzyme(r1, e2);
+
+ assertTrue("r1 and r2 must be identified as redundant", BioReactionUtils.areRedundant(network, r1, r2, false));
+ assertFalse("r1 and r2 must be identified as not redundant, considering GPR", BioReactionUtils.areRedundant(network, r1, r2, true));
+
+ network.affectEnzyme(r2, e1);
+ network.affectEnzyme(r2, e2);
+ assertTrue("r1 and r2 must be identified as redundant, considering GPR", BioReactionUtils.areRedundant(network, r1, r2, true));
+
+ }
+
@Test
public void testAreRedundantReversible() {
--
GitLab
From cfb6cc74a7ee9289b229fa4795cd2e605ddeaf3c Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 22 Jun 2023 13:21:23 +0200
Subject: [PATCH 11/13] add isolated node removal and duplicated reaction
removal options in ProcessSBML
---
.../met4j_toolbox/convert/ProcessSBML.java | 29 ++++++++++++++-----
1 file changed, 22 insertions(+), 7 deletions(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
index fbe114e50..0dd746251 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
@@ -2,6 +2,7 @@ package fr.inrae.toulouse.metexplore.met4j_toolbox.convert;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.utils.BioNetworkUtils;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.utils.CompartmentMerger;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.*;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.EdgeMerger;
@@ -49,6 +50,9 @@ public class ProcessSBML extends AbstractMet4jApplication {
@Option(name = "-rc", usage = "remove compounds from input identifier file", required = false)
public String inputSide = null;
+ @Option(name = "-ric", aliases = {"--noIsolated"}, usage = "remove isolated compounds (not involved in any reaction)")
+ public boolean removeIsolated;
+
@ParameterType(name = EnumParameterTypes.InputFile)
@Format(name = EnumFormats.Txt)
@Option(name = "-rr", usage = "remove reaction from input identifier file", required = false)
@@ -67,7 +71,9 @@ public class ProcessSBML extends AbstractMet4jApplication {
@Option(name = "-mc", aliases = {"--mergecomp"}, usage = "merge compartments. " +
"Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form \"xxx_y\" with xxx as base identifier and y as compartment label).")
public strategy mergingStrat = strategy.no;
- public String idRegex = "^(\\w+)_\\w$";
+
+ @Option(name = "-rdr", aliases = {"--noDuplicated"}, usage = "remove duplicated reactions (same reactants, same GPR)")
+ public boolean removeDuplicated;
@Option(name = "-rEX", aliases = {"--removeExchange"}, usage = "remove exchange reactions and species from given exchange compartment identifier", required = false)
@@ -185,16 +191,19 @@ public class ProcessSBML extends AbstractMet4jApplication {
}
}
+
+ //remove compounds not in any reactions
+ if(removeIsolated){
+ System.err.println("removing isolated compounds...");
+ BioNetworkUtils.removeNotConnectedMetabolites(network);
+ }
+
//merge compartment
BioNetwork newNetwork;
if (mergingStrat == strategy.by_id) {
System.err.print("Merging compartments...");
CompartmentMerger merger = new CompartmentMerger()
- .setGetUniqIdFunction(c -> c.getId().substring(0,c.getId().length()-2))
- .setCompoundMergeFunction((l -> {
- BioMetabolite oldComp = l.get(0);
- return new BioMetabolite(oldComp,oldComp.getId().substring(0,oldComp.getId().length()-2));
- }));
+ .usePalssonIdentifierConvention();
newNetwork = merger.merge(network);
System.err.println(" Done.");
}else if (mergingStrat != strategy.by_name) {
@@ -207,6 +216,12 @@ public class ProcessSBML extends AbstractMet4jApplication {
newNetwork = network;
}
+ //remove duplicated reactions
+ if(removeDuplicated){
+ System.err.println("removing duplicated reactions...");
+ BioNetworkUtils.removeDuplicatedReactions(newNetwork,true);
+ }
+
//print info
System.out.println("\tcompartments:\t"+newNetwork.getCompartmentsView().size());
System.out.println("\tmetabolites:\t"+newNetwork.getMetabolitesView().size());
@@ -230,7 +245,7 @@ public class ProcessSBML extends AbstractMet4jApplication {
@Override
public String getLongDescription() {
- return "General SBML model processing including compound removal (such as side compounds), reaction removal (blocked or exchange reaction), and compartments merging";
+ return "General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartments merging";
}
@Override
--
GitLab
From 338c7facf21f4aa83fd00c8673cd6d1ab9b3ba4c Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Fri, 23 Jun 2023 15:36:49 +0200
Subject: [PATCH 12/13] Optimize Redundant reactions removal + add test
---
.../biodata/utils/BioNetworkUtils.java | 20 +++++++--------
.../biodata/utils/BioNetworkUtilsTest.java | 25 +++++++++++++++++++
2 files changed, 35 insertions(+), 10 deletions(-)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
index bf66a9cbb..6753f34f6 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
@@ -111,17 +111,17 @@ public class BioNetworkUtils {
* @param checkSameGPR if reactions should be considered non-redundant if they share same reactants but have different GPR
*/
public static void removeDuplicatedReactions(@NonNull BioNetwork network, boolean checkSameGPR) {
- ArrayList<BioReaction> reactions = new ArrayList<>(network.getReactionsView());
- BioCollection<BioReaction> toRemove = new BioCollection<>();
- for (int i = 0; i < reactions.size(); i++){
- for (int j = i + 1; j < reactions.size(); j++) {
- BioReaction r1 = reactions.get(i);
- BioReaction r2 = reactions.get(j);
- if(BioReactionUtils.areRedundant(network,r1,r2,checkSameGPR)){
- toRemove.add(r1);
- }
- }
+ //1- for each reaction, create an id from equation and, optionally, GPR
+ //2- put id-reaction pairs in map, each new reaction overrides its duplicates, if any
+ //3- remove from network all reactions not in map
+ HashMap<String,BioReaction> indexedReaction = new HashMap<>();
+ BioCollection<BioReaction> toRemove = new BioCollection<>(network.getReactionsView());
+ for (BioReaction r : network.getReactionsView()){
+ String uniqId = BioReactionUtils.getEquation(r,false,true);
+ if(checkSameGPR) uniqId = uniqId+BioReactionUtils.getGPR(network,r);
+ indexedReaction.put(uniqId,r);
}
+ toRemove.removeAll(indexedReaction.values());
network.removeOnCascade(toRemove);
}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java
index bc9c6f2eb..3220ce16e 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java
@@ -94,6 +94,31 @@ public class BioNetworkUtilsTest {
}
+ @Test
+ public void testRemoveDuplicatedReactions(){
+ BioNetwork network = miniNetwork();
+ BioReaction r3 = new BioReaction("R3");
+ network.add(r3);
+ network.affectLeft(r3, 2.0, c1, m1);
+ network.affectRight(r3, 1.0, c1, m2);
+
+ BioNetworkUtils.removeDuplicatedReactions(network,false);
+ assertFalse("Duplicated reaction not removed",network.containsReaction("R3"));
+
+ r3 = new BioReaction("R3");
+ network.add(r3);
+ network.affectLeft(r3, 2.0, c1, m1);
+ network.affectRight(r3, 1.0, c1, m2);
+
+ BioNetworkUtils.removeDuplicatedReactions(network,true);
+ assertTrue("Non-duplicated reaction (considering GPR) removed",network.containsReaction("R3"));
+
+ network.affectEnzyme(r3, enzyme1);
+
+ BioNetworkUtils.removeDuplicatedReactions(network,true);
+ assertFalse("Duplicated reaction (considering GPR) not removed",network.containsReaction("R3"));
+ }
+
@Test
public void removeNotConnectedMetabolites() {
--
GitLab
From 4adeeb81bf3ad992f9c90d0b3c9b7058c6ceb9ea Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Fri, 23 Jun 2023 15:48:03 +0200
Subject: [PATCH 13/13] rename app, clean imports, improve console output
---
.../{ProcessSBML.java => SBMLwizard.java} | 31 +++++++------------
1 file changed, 11 insertions(+), 20 deletions(-)
rename met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/{ProcessSBML.java => SBMLwizard.java} (88%)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/SBMLwizard.java
similarity index 88%
rename from met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
rename to met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/SBMLwizard.java
index 0dd746251..a44ce464c 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/ProcessSBML.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/convert/SBMLwizard.java
@@ -4,16 +4,6 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.utils.BioNetworkUtils;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.utils.CompartmentMerger;
-import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.*;
-import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.EdgeMerger;
-import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.VertexContraction;
-import fr.inrae.toulouse.metexplore.met4j_graph.computation.utils.ComputeAdjacencyMatrix;
-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.ExportGraph;
-import fr.inrae.toulouse.metexplore.met4j_graph.io.NodeMapping;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.ReactionAttributes;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
@@ -24,21 +14,18 @@ import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.PackageParser;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.JsbmlWriter;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.Met4jSbmlWriterException;
import fr.inrae.toulouse.metexplore.met4j_mapping.Mapper;
-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.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 fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis.CompoundNet;
import org.kohsuke.args4j.Option;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashSet;
-public class ProcessSBML extends AbstractMet4jApplication {
+public class SBMLwizard extends AbstractMet4jApplication {
@Format(name = EnumFormats.Sbml)
@ParameterType(name = EnumParameterTypes.InputFile)
@@ -81,7 +68,7 @@ public class ProcessSBML extends AbstractMet4jApplication {
public static void main(String[] args) throws Met4jSbmlWriterException, IOException {
- ProcessSBML app = new ProcessSBML();
+ SBMLwizard app = new SBMLwizard();
app.parseArguments(args);
@@ -108,13 +95,13 @@ public class ProcessSBML extends AbstractMet4jApplication {
System.out.println(" Done.");
//print info
- System.out.println("\tcompartments:\t"+network.getCompartmentsView().size());
+ System.out.println("\n\n\tcompartments:\t"+network.getCompartmentsView().size());
System.out.println("\tmetabolites:\t"+network.getMetabolitesView().size());
System.out.println("\treactions:\t"+network.getReactionsView().size());
System.out.println("\tenzymes:\t"+network.getEnzymesView().size());
System.out.println("\tgenes:\t"+network.getGenesView().size());
System.out.println("\tprotein:\t"+network.getProteinsView().size());
- System.out.println("\tpathway:\t"+network.getPathwaysView().size());
+ System.out.println("\tpathway:\t"+network.getPathwaysView().size()+"\n\n");
//side compound removal [optional]
if (inputSide != null) {
@@ -172,7 +159,7 @@ public class ProcessSBML extends AbstractMet4jApplication {
}
network.removeOnCascade(toRemove);
- System.err.println(toRemove.size() + " external species removed from network.");
+ System.err.println(toRemove.size() + " \"closed\" reactions removed from network.");
}
//exchange reaction removal
@@ -195,7 +182,9 @@ public class ProcessSBML extends AbstractMet4jApplication {
//remove compounds not in any reactions
if(removeIsolated){
System.err.println("removing isolated compounds...");
+ int n = network.getMetabolitesView().size();
BioNetworkUtils.removeNotConnectedMetabolites(network);
+ System.err.println((n-network.getMetabolitesView().size())+" isolated compounds removed from network.");
}
//merge compartment
@@ -219,17 +208,19 @@ public class ProcessSBML extends AbstractMet4jApplication {
//remove duplicated reactions
if(removeDuplicated){
System.err.println("removing duplicated reactions...");
+ int n = network.getReactionsView().size();
BioNetworkUtils.removeDuplicatedReactions(newNetwork,true);
+ System.err.println((n-network.getMetabolitesView().size())+" duplicated reactions removed from network.");
}
//print info
- System.out.println("\tcompartments:\t"+newNetwork.getCompartmentsView().size());
+ System.out.println("\n\n\tcompartments:\t"+newNetwork.getCompartmentsView().size());
System.out.println("\tmetabolites:\t"+newNetwork.getMetabolitesView().size());
System.out.println("\treactions:\t"+newNetwork.getReactionsView().size());
System.out.println("\tenzymes:\t"+newNetwork.getEnzymesView().size());
System.out.println("\tgenes:\t"+newNetwork.getGenesView().size());
System.out.println("\tprotein:\t"+newNetwork.getProteinsView().size());
- System.out.println("\tpathway:\t"+newNetwork.getPathwaysView().size());
+ System.out.println("\tpathway:\t"+newNetwork.getPathwaysView().size()+"\n\n");
//export network
System.out.print("Exporting...");
--
GitLab