From c0ddcc203ca278f18d8b797ad3979a852e8337e1 Mon Sep 17 00:00:00 2001
From: LouisonF <fresnaislouison@gmail.com>
Date: Wed, 12 Oct 2022 19:04:49 +0200
Subject: [PATCH 1/8] add getReactionSudeCompounds public method
---
.../connect/weighting/RPAIRSlikePolicy.java | 42 +++++++++++++++++--
1 file changed, 39 insertions(+), 3 deletions(-)
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
index 269cbcf03..1049bd9dd 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
@@ -3,11 +3,10 @@ package fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting;
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.BioReaction;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.analyze.GraphMeasure;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.GraphFilter;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.BioGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
-import fr.inrae.toulouse.metexplore.met4j_graph.core.GraphFactory;
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;
@@ -34,6 +33,44 @@ public class RPAIRSlikePolicy extends WeightingPolicy<BioMetabolite, ReactionEdg
preprocess.removeNotFound=false;
}
+ /**
+ * get Reaction specific side compounds from edge weights
+ * @return rSideCpds
+ */
+ public HashMap<BioReaction,BioCollection<BioMetabolite>> getReactionSideCompounds(CompoundGraph compoundGraph){
+ HashMap<BioReaction,BioCollection<BioMetabolite>> rSideCpds = new HashMap<>();
+ HashMap<String,BioReaction> rList = compoundGraph.getBiochemicalReactionList();
+ HashMap<ReactionEdge,Double> weightMap = compoundGraph.getEdgeWeightMap();
+ for(ReactionEdge test : weightMap.keySet()){
+ System.out.println(test.getV1()+" / "+test.getV2()+" / "+weightMap.get(test).toString()+" / "+test.getReaction().getId());
+ }
+ //To be able to identy side compounds from side and spurious edges (that are not in the csn)
+ //we need to consider every cpd not main as side, reaction-wise.
+
+ for(BioReaction tmpR : rList.values()){
+ //get all weightMap entry for edges associated with this reaction
+ BioCollection<BioMetabolite> tmpMain = new BioCollection<>();
+ for(ReactionEdge rEdge : compoundGraph.getEdgesFromReaction(tmpR.getId())){
+ if(weightMap.get(rEdge).equals(mainValue)){
+ tmpMain.add(rEdge.getV1());
+ tmpMain.add(rEdge.getV2());
+ }
+ }
+ //get all metabolites associated with this reaction
+ BioCollection<BioMetabolite> rMets = tmpR.getMetabolitesView();
+ //remove main metabolites from rMets
+ rMets.removeAll(tmpMain);
+ if(rMets.size()>0){
+ if(rSideCpds.containsKey(tmpR)){
+ rSideCpds.get(tmpR).addAll(rMets);
+ }else{
+ rSideCpds.put(tmpR, rMets);
+ }
+ }
+ }
+ return rSideCpds;
+ }
+
/**
* remove side transitions , estimated from edge redundancy
* @return
@@ -76,7 +113,6 @@ public class RPAIRSlikePolicy extends WeightingPolicy<BioMetabolite, ReactionEdg
compoundGraph.setEdgeWeight(e,sideValue);
}
}
-
if(removeSide){
GraphFilter.weightFilter(compoundGraph,sideValue,GraphFilter.EQUALITY);
}
--
GitLab
From 597ccf795a335c508026850ee184026b05dad05c Mon Sep 17 00:00:00 2001
From: LouisonF <fresnaislouison@gmail.com>
Date: Wed, 12 Oct 2022 19:06:02 +0200
Subject: [PATCH 2/8] add getReactionGraph overload
---
.../met4j_graph/io/Bionetwork2BioGraph.java | 48 +++++++++++++++++++
1 file changed, 48 insertions(+)
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
index b2515df34..86ab7e080 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
@@ -161,6 +161,54 @@ public class Bionetwork2BioGraph {
return g;
}
+ /**
+ * Builds the graph.
+ *
+ * @param rcofactors a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} object.
+ * @return a {@link fr.inrae.toulouse.metexplore.met4j_graph.core.reaction.ReactionGraph} object.
+ */
+ public ReactionGraph getReactionGraph(HashMap<BioReaction,BioCollection<BioMetabolite>> rcofactors){
+
+ ReactionGraph g = new ReactionGraph();
+ HashMap<BioMetabolite,BioCollection<BioReaction>> consumingReaction = new HashMap<>();
+ HashMap<BioMetabolite,BioCollection<BioReaction>> productingReaction = new HashMap<>();
+
+ for(BioReaction r : bn.getReactionsView()){
+ if(!r.getLeftsView().isEmpty() && !r.getRightsView().isEmpty()) {
+ g.addVertex(r);
+ BioCollection<BioMetabolite> rLeftView = r.getLeftsView();
+ BioCollection<BioMetabolite> rRightView = r.getRightsView();
+ if(!Objects.isNull(rcofactors.get(r))){
+ rLeftView.removeAll(rcofactors.get(r));
+ rRightView.removeAll(rcofactors.get(r));
+ }
+ rLeftView.forEach(s -> {
+ consumingReaction.computeIfAbsent(s, k -> new BioCollection<>()).add(r);
+ if (r.isReversible()) {
+ productingReaction.computeIfAbsent(s, k -> new BioCollection<>()).add(r);
+ }
+ });
+
+ rRightView.forEach(p -> {
+ productingReaction.computeIfAbsent(p, k -> new BioCollection<>()).add(r);
+ if (r.isReversible()) {
+ consumingReaction.computeIfAbsent(p, k -> new BioCollection<>()).add(r);
+ }
+ });
+ }
+ }
+
+ consumingReaction.keySet().retainAll(productingReaction.keySet());
+
+ consumingReaction.forEach((c, sources) -> sources.forEach((r1) -> {
+ productingReaction.get(c).forEach(r2 -> {
+
+ if(r1!=r2) g.addEdge(r2,r1,new CompoundEdge(r2,r1,c));
+
+ });
+ }));
+ return g;
+ }
/**
* <p>getBipartiteGraph.</p>
--
GitLab
From a1a738bc37ddc202ac74d37229012ff42aaca7bc Mon Sep 17 00:00:00 2001
From: LouisonF <fresnaislouison@gmail.com>
Date: Wed, 12 Oct 2022 19:07:21 +0200
Subject: [PATCH 3/8] add RPAIRS and ReactionGraph options
---
.../networkAnalysis/CarbonSkeletonNet.java | 87 ++++++++++++++++++-
1 file changed, 83 insertions(+), 4 deletions(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
index 043e7d799..19208ffdb 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
@@ -3,13 +3,16 @@ package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
import fr.inrae.toulouse.metexplore.met4j_chemUtils.FormulaParser;
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.weighting.AtomMappingWeightPolicy;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.RPAIRSlikePolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.ReactionProbabilityWeight;
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.computation.transform.GraphOperation;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.reaction.ReactionGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.io.Bionetwork2BioGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.io.ExportGraph;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
@@ -22,13 +25,20 @@ 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.apache.commons.lang3.StringUtils;
import org.kohsuke.args4j.Option;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
import java.io.IOException;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Objects;
import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.*;
import static fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumFormats.Sbml;
@@ -72,10 +82,19 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
@Option(name = "-am", aliases = {"--asmatrix"}, usage = "export as matrix (implies simple graph conversion). Default export as GML file", required = false)
public boolean asMatrix = false;
+ @Option(name = "-rf", aliases = {"--reactionscps"}, usage = "input Reaction Side compounds file", required = false)
+ public String reactionSideCompoundsFile = null;
+
+ @Option(name = "-rg", aliases = {"--reactiongraph"}, usage = "export the reaction graph of the carbon skeleton network", required = false)
+ public boolean reactiongraph = false;
+
+ @Option(name = "-ws", aliases = {"--writeReactionSideCompounds"}, usage = "export the list of reaction side compounds in a tabulated file", required = false)
+ public boolean writeReactionSideCompounds = false;
+
@Option(name = "-i", aliases = {"--fromIndexes"}, usage = "Use GSAM output with carbon indexes", required = false)
public boolean fromIndexes = false;
- public static void main(String[] args) {
+ public static void main(String[] args) throws IOException, Met4jSbmlReaderException {
CarbonSkeletonNet app = new CarbonSkeletonNet();
@@ -86,7 +105,7 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
}
- public void run() {
+ public void run() throws IOException, Met4jSbmlReaderException {
System.out.print("Reading SBML...");
JsbmlReader reader = new JsbmlReader(this.inputPath);
ArrayList<PackageParser> pkgs = new ArrayList<>(Arrays.asList(
@@ -184,6 +203,66 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
System.out.println(" Done.");
}
+ //get the reaction graph
+ if(reactiongraph){
+ //instanciate rgraph variable
+ ReactionGraph rgraph;
+ if(!Objects.isNull(reactionSideCompoundsFile)){
+ //create the hashmap
+ HashMap<BioReaction,BioCollection<BioMetabolite>> reactionSideCompounds = new HashMap<BioReaction,BioCollection<BioMetabolite>>();
+ BufferedReader rscpsReader = new BufferedReader(new FileReader(reactionSideCompoundsFile));
+ String currentLine;
+ //get the Biochemical reaction list
+ HashMap<String,BioReaction> ReactionMap = graph.getBiochemicalReactionList();
+ //Read each line and fill the Reaction Side Compounds Hashmap
+ while ((currentLine = rscpsReader.readLine()) != null){
+ String[] splitLine = currentLine.split("\t");
+ BioCollection<BioMetabolite> scpsSet = new BioCollection<BioMetabolite>();
+ for(String met : splitLine[1].replaceAll("[\\[\\]]", "").split(",")){
+ scpsSet.add(graph.getVertex(met));
+ System.out.println(met);
+ }
+ reactionSideCompounds.put(ReactionMap.get(splitLine[0]), scpsSet);
+ }
+ rscpsReader.close();
+ rgraph = builder.getReactionGraph(reactionSideCompounds);
+ }else{
+ RPAIRSlikePolicy rp = new RPAIRSlikePolicy(wp);
+ rp.setWeight(graph);
+ HashMap<BioReaction,BioCollection<BioMetabolite>> reactionSideCompounds = rp.getReactionSideCompounds(graph);
+ rgraph = builder.getReactionGraph(reactionSideCompounds);
+ }
+ ExportGraph.toGmlWithAttributes(rgraph, "reactiongraph_"+this.outputPath, true);
+ }
+
+ //write reaction side compounds
+ if(writeReactionSideCompounds){
+ RPAIRSlikePolicy rp = new RPAIRSlikePolicy(wp);
+ rp.setWeight(graph);
+ HashMap<BioReaction,BioCollection<BioMetabolite>> reactionSideCompounds = rp.getReactionSideCompounds(graph);
+ BufferedWriter fw = new BufferedWriter(new FileWriter("reactionSCs_"+outputPath.replace(".gml", ".tab"),false),8*1024);
+ try{
+ fw.write("ReactionID\tSideCpds\n");
+ for(BioReaction elem : reactionSideCompounds.keySet()){
+ //Instanciate iterator
+ Iterator<BioMetabolite> it = reactionSideCompounds.get(elem).iterator();
+ fw.write(elem.getId()+"\t");
+ while(it.hasNext()){
+ String met = it.next().getId();
+ if(it.hasNext()){
+ fw.write(met+",");
+ }else{
+ fw.write(met);
+ }
+ }
+ fw.write("\n");
+ }
+ fw.close();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
//export graph
System.out.print("Exporting...");
if (asMatrix) {
--
GitLab
From bf9cc47bbad559d27e577e00a42e61cb551e6dfb Mon Sep 17 00:00:00 2001
From: LouisonF <fresnaislouison@gmail.com>
Date: Thu, 13 Oct 2022 08:48:12 +0200
Subject: [PATCH 4/8] remove debugging verbose in getReactionSideCompounds
---
.../computation/connect/weighting/RPAIRSlikePolicy.java | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
index 1049bd9dd..af3c43d16 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
@@ -39,15 +39,11 @@ public class RPAIRSlikePolicy extends WeightingPolicy<BioMetabolite, ReactionEdg
*/
public HashMap<BioReaction,BioCollection<BioMetabolite>> getReactionSideCompounds(CompoundGraph compoundGraph){
HashMap<BioReaction,BioCollection<BioMetabolite>> rSideCpds = new HashMap<>();
- HashMap<String,BioReaction> rList = compoundGraph.getBiochemicalReactionList();
HashMap<ReactionEdge,Double> weightMap = compoundGraph.getEdgeWeightMap();
- for(ReactionEdge test : weightMap.keySet()){
- System.out.println(test.getV1()+" / "+test.getV2()+" / "+weightMap.get(test).toString()+" / "+test.getReaction().getId());
- }
//To be able to identy side compounds from side and spurious edges (that are not in the csn)
//we need to consider every cpd not main as side, reaction-wise.
- for(BioReaction tmpR : rList.values()){
+ for(BioReaction tmpR : compoundGraph.getBiochemicalReactionList().values()){
//get all weightMap entry for edges associated with this reaction
BioCollection<BioMetabolite> tmpMain = new BioCollection<>();
for(ReactionEdge rEdge : compoundGraph.getEdgesFromReaction(tmpR.getId())){
--
GitLab
From e2e098907411917f4d52348cf86ea6c6fef1ea90 Mon Sep 17 00:00:00 2001
From: LouisonF <fresnaislouison@gmail.com>
Date: Thu, 13 Oct 2022 10:00:59 +0200
Subject: [PATCH 5/8] Add a globalsidecompound feature (to remove CoA)
---
.../met4j_graph/io/Bionetwork2BioGraph.java | 55 ++++++++++++++++++-
.../networkAnalysis/CarbonSkeletonNet.java | 20 +++++--
2 files changed, 70 insertions(+), 5 deletions(-)
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
index 86ab7e080..d236dd10e 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
@@ -164,7 +164,7 @@ public class Bionetwork2BioGraph {
/**
* Builds the graph.
*
- * @param rcofactors a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} object.
+ * @param rcofactors a {@link java.util.HashMap } object.
* @return a {@link fr.inrae.toulouse.metexplore.met4j_graph.core.reaction.ReactionGraph} object.
*/
public ReactionGraph getReactionGraph(HashMap<BioReaction,BioCollection<BioMetabolite>> rcofactors){
@@ -210,6 +210,59 @@ public class Bionetwork2BioGraph {
return g;
}
+ /**
+ * Builds the graph.
+ *
+ * @param rcofactors a {@link java.util.HashMap} object.
+ * @param globalcofactors a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} object.
+ * @return a {@link fr.inrae.toulouse.metexplore.met4j_graph.core.reaction.ReactionGraph} object.
+ */
+ public ReactionGraph getReactionGraph(HashMap<BioReaction,BioCollection<BioMetabolite>> rcofactors, BioCollection<BioMetabolite> globalcofactors){
+
+ ReactionGraph g = new ReactionGraph();
+ HashMap<BioMetabolite,BioCollection<BioReaction>> consumingReaction = new HashMap<>();
+ HashMap<BioMetabolite,BioCollection<BioReaction>> productingReaction = new HashMap<>();
+
+ for(BioReaction r : bn.getReactionsView()){
+ if(!r.getLeftsView().isEmpty() && !r.getRightsView().isEmpty()) {
+ g.addVertex(r);
+ BioCollection<BioMetabolite> rLeftView = r.getLeftsView();
+ BioCollection<BioMetabolite> rRightView = r.getRightsView();
+ if(!Objects.isNull(rcofactors.get(r))){
+ rLeftView.removeAll(rcofactors.get(r));
+ rRightView.removeAll(rcofactors.get(r));
+ }
+ rLeftView.forEach(s -> {
+ consumingReaction.computeIfAbsent(s, k -> new BioCollection<>()).add(r);
+ if (r.isReversible()) {
+ productingReaction.computeIfAbsent(s, k -> new BioCollection<>()).add(r);
+ }
+ });
+
+ rRightView.forEach(p -> {
+ productingReaction.computeIfAbsent(p, k -> new BioCollection<>()).add(r);
+ if (r.isReversible()) {
+ consumingReaction.computeIfAbsent(p, k -> new BioCollection<>()).add(r);
+ }
+ });
+ }
+ }
+
+ if(!Objects.isNull(globalcofactors)){
+ consumingReaction.keySet().removeAll(globalcofactors);
+ productingReaction.keySet().removeAll(globalcofactors);
+ }
+ consumingReaction.keySet().retainAll(productingReaction.keySet());
+
+ consumingReaction.forEach((c, sources) -> sources.forEach((r1) -> {
+ productingReaction.get(c).forEach(r2 -> {
+
+ if(r1!=r2) g.addEdge(r2,r1,new CompoundEdge(r2,r1,c));
+
+ });
+ }));
+ return g;
+ }
/**
* <p>getBipartiteGraph.</p>
*
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
index 19208ffdb..86807029e 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
@@ -12,9 +12,11 @@ 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.compound.CompoundGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.reaction.ReactionGraph;
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;
@@ -84,6 +86,9 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
@Option(name = "-rf", aliases = {"--reactionscps"}, usage = "input Reaction Side compounds file", required = false)
public String reactionSideCompoundsFile = null;
+
+ @Option(name = "-gs", aliases = {"--globalscps"}, usage = "input Global Side compounds file", required = false)
+ public String globalSideCompoundsFile = null;
@Option(name = "-rg", aliases = {"--reactiongraph"}, usage = "export the reaction graph of the carbon skeleton network", required = false)
public boolean reactiongraph = false;
@@ -207,9 +212,9 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
if(reactiongraph){
//instanciate rgraph variable
ReactionGraph rgraph;
+ //create the hashmap
+ HashMap<BioReaction,BioCollection<BioMetabolite>> reactionSideCompounds = new HashMap<BioReaction,BioCollection<BioMetabolite>>();
if(!Objects.isNull(reactionSideCompoundsFile)){
- //create the hashmap
- HashMap<BioReaction,BioCollection<BioMetabolite>> reactionSideCompounds = new HashMap<BioReaction,BioCollection<BioMetabolite>>();
BufferedReader rscpsReader = new BufferedReader(new FileReader(reactionSideCompoundsFile));
String currentLine;
//get the Biochemical reaction list
@@ -225,11 +230,18 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
reactionSideCompounds.put(ReactionMap.get(splitLine[0]), scpsSet);
}
rscpsReader.close();
- rgraph = builder.getReactionGraph(reactionSideCompounds);
}else{
RPAIRSlikePolicy rp = new RPAIRSlikePolicy(wp);
rp.setWeight(graph);
- HashMap<BioReaction,BioCollection<BioMetabolite>> reactionSideCompounds = rp.getReactionSideCompounds(graph);
+ reactionSideCompounds = rp.getReactionSideCompounds(graph);
+ }
+ //If a globalSideCompounds file is provided
+ if(!Objects.isNull(globalSideCompoundsFile)){
+ //read content of file
+ NodeMapping<BioMetabolite, ReactionEdge, CompoundGraph> mapper = new NodeMapping<>(graph).skipIfNotFound();
+ BioCollection<BioMetabolite> sideCpds = mapper.map(globalSideCompoundsFile);
+ rgraph = builder.getReactionGraph(reactionSideCompounds,sideCpds);
+ }else{
rgraph = builder.getReactionGraph(reactionSideCompounds);
}
ExportGraph.toGmlWithAttributes(rgraph, "reactiongraph_"+this.outputPath, true);
--
GitLab
From b32ea655de109ac6a3e876ca766ed562d5763aa4 Mon Sep 17 00:00:00 2001
From: LouisonF <fresnaislouison@gmail.com>
Date: Thu, 13 Oct 2022 18:11:45 +0200
Subject: [PATCH 6/8] add getReactionMainCompounds
---
.../connect/weighting/RPAIRSlikePolicy.java | 39 +++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
index af3c43d16..b032ff8d9 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/RPAIRSlikePolicy.java
@@ -62,11 +62,50 @@ public class RPAIRSlikePolicy extends WeightingPolicy<BioMetabolite, ReactionEdg
}else{
rSideCpds.put(tmpR, rMets);
}
+ }else{
+ if(!rSideCpds.containsKey(tmpR)){
+ rSideCpds.put(tmpR, null);
+ }
}
}
return rSideCpds;
}
+ /**
+ * get Reaction specific main compounds from edge weights
+ * @return rSideCpds
+ */
+ public HashMap<BioReaction,BioCollection<BioMetabolite>> getReactionMainCompounds(CompoundGraph compoundGraph){
+ HashMap<BioReaction,BioCollection<BioMetabolite>> rMainCpds = new HashMap<>();
+ HashMap<ReactionEdge,Double> weightMap = compoundGraph.getEdgeWeightMap();
+ //To be able to identy side compounds from side and spurious edges (that are not in the csn)
+ //we need to consider every cpd not main as side, reaction-wise.
+
+ for(BioReaction tmpR : compoundGraph.getBiochemicalReactionList().values()){
+ //get all weightMap entry for edges associated with this reaction
+ BioCollection<BioMetabolite> tmpMain = new BioCollection<>();
+ for(ReactionEdge rEdge : compoundGraph.getEdgesFromReaction(tmpR.getId())){
+ if(weightMap.get(rEdge).equals(mainValue)){
+ tmpMain.add(rEdge.getV1());
+ tmpMain.add(rEdge.getV2());
+ }
+ }
+ if(tmpMain.size()>0){
+ if(rMainCpds.containsKey(tmpR)){
+ rMainCpds.get(tmpR).addAll(tmpMain);
+ }else{
+ rMainCpds.put(tmpR, tmpMain);
+ }
+ }
+ // }else{
+ // if(!rSideCpds.containsKey(tmpR)){
+ // rSideCpds.put(tmpR, null);
+ // }
+ // }
+ }
+ return rMainCpds;
+ }
+
/**
* remove side transitions , estimated from edge redundancy
* @return
--
GitLab
From 17aaaeeb8fe45cd7a15c7941229531e19f319e42 Mon Sep 17 00:00:00 2001
From: LouisonF <fresnaislouison@gmail.com>
Date: Thu, 13 Oct 2022 18:12:38 +0200
Subject: [PATCH 7/8] Add getSimplifiedReactionGraph option
---
.../met4j_graph/io/Bionetwork2BioGraph.java | 80 ++++++++++++++++---
1 file changed, 71 insertions(+), 9 deletions(-)
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
index d236dd10e..2bfe15210 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
@@ -174,7 +174,9 @@ public class Bionetwork2BioGraph {
HashMap<BioMetabolite,BioCollection<BioReaction>> productingReaction = new HashMap<>();
for(BioReaction r : bn.getReactionsView()){
- if(!r.getLeftsView().isEmpty() && !r.getRightsView().isEmpty()) {
+ //check that current reaction have metabolites and is in the rcofactors map
+ //(if not it means that there is no mention of this reaction in the CSN)
+ if(!r.getLeftsView().isEmpty() && !r.getRightsView().isEmpty() && rcofactors.keySet().contains(r)) {
g.addVertex(r);
BioCollection<BioMetabolite> rLeftView = r.getLeftsView();
BioCollection<BioMetabolite> rRightView = r.getRightsView();
@@ -224,14 +226,16 @@ public class Bionetwork2BioGraph {
HashMap<BioMetabolite,BioCollection<BioReaction>> productingReaction = new HashMap<>();
for(BioReaction r : bn.getReactionsView()){
- if(!r.getLeftsView().isEmpty() && !r.getRightsView().isEmpty()) {
+ //check that current reaction have metabolites and is in the rcofactors map
+ //(if not it means that there is no mention of this reaction in the CSN)
+ BioCollection<BioMetabolite> rLeftView = r.getLeftsView();
+ BioCollection<BioMetabolite> rRightView = r.getRightsView();
+ if(!Objects.isNull(rcofactors.get(r))){
+ rLeftView.removeAll(rcofactors.get(r));
+ rRightView.removeAll(rcofactors.get(r));
+ }
+ if(!rLeftView.isEmpty() && !rRightView.isEmpty() && rcofactors.keySet().contains(r)) {
g.addVertex(r);
- BioCollection<BioMetabolite> rLeftView = r.getLeftsView();
- BioCollection<BioMetabolite> rRightView = r.getRightsView();
- if(!Objects.isNull(rcofactors.get(r))){
- rLeftView.removeAll(rcofactors.get(r));
- rRightView.removeAll(rcofactors.get(r));
- }
rLeftView.forEach(s -> {
consumingReaction.computeIfAbsent(s, k -> new BioCollection<>()).add(r);
if (r.isReversible()) {
@@ -239,7 +243,7 @@ public class Bionetwork2BioGraph {
}
});
- rRightView.forEach(p -> {
+ rRightView.forEach(p -> {
productingReaction.computeIfAbsent(p, k -> new BioCollection<>()).add(r);
if (r.isReversible()) {
consumingReaction.computeIfAbsent(p, k -> new BioCollection<>()).add(r);
@@ -263,6 +267,64 @@ public class Bionetwork2BioGraph {
}));
return g;
}
+
+ /**
+ * Builds the graph.
+ *
+ * @param rcofactors a {@link java.util.HashMap} object.
+ * @param globalcofactors a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} object.
+ * @return a {@link fr.inrae.toulouse.metexplore.met4j_graph.core.reaction.ReactionGraph} object.
+ */
+ public ReactionGraph getSimplifiedReactionGraph(HashMap<BioReaction,BioCollection<BioMetabolite>> rcofactors, BioCollection<BioMetabolite> globalcofactors){
+
+ ReactionGraph g = new ReactionGraph();
+ HashMap<BioMetabolite,BioCollection<BioReaction>> consumingReaction = new HashMap<>();
+ HashMap<BioMetabolite,BioCollection<BioReaction>> productingReaction = new HashMap<>();
+
+ for(BioReaction r : bn.getReactionsView()){
+ //check that current reaction have metabolites and is in the rcofactors map
+ //(if not it means that there is no mention of this reaction in the CSN)
+ BioCollection<BioMetabolite> rLeftView = r.getLeftsView();
+ BioCollection<BioMetabolite> rRightView = r.getRightsView();
+ if(!Objects.isNull(rcofactors.get(r))){
+ rLeftView.removeAll(rcofactors.get(r));
+ rRightView.removeAll(rcofactors.get(r));
+ }
+ if(!rLeftView.isEmpty() && !rRightView.isEmpty() && rcofactors.keySet().contains(r)) {
+ g.addVertex(r);
+ rLeftView.forEach(s -> {
+ consumingReaction.computeIfAbsent(s, k -> new BioCollection<>()).add(r);
+ if (r.isReversible()) {
+ productingReaction.computeIfAbsent(s, k -> new BioCollection<>()).add(r);
+ }
+ });
+
+ rRightView.forEach(p -> {
+ productingReaction.computeIfAbsent(p, k -> new BioCollection<>()).add(r);
+ if (r.isReversible()) {
+ consumingReaction.computeIfAbsent(p, k -> new BioCollection<>()).add(r);
+ }
+ });
+ }
+ }
+
+ if(!Objects.isNull(globalcofactors)){
+ consumingReaction.keySet().removeAll(globalcofactors);
+ productingReaction.keySet().removeAll(globalcofactors);
+ }
+ consumingReaction.keySet().retainAll(productingReaction.keySet());
+
+ consumingReaction.forEach((c, sources) -> sources.forEach((r1) -> {
+ productingReaction.get(c).forEach(r2 -> {
+ if(r1 != r2 && Objects.isNull(g.getEdge(r1.getId(), r2.getId(),c.getId())) && Objects.isNull(g.getEdge(r2.getId(), r1.getId(),c.getId()))){
+ g.addEdge(r2,r1,new CompoundEdge(r2,r1,c));
+ }
+ });
+ }));
+ return g;
+ }
+
+
/**
* <p>getBipartiteGraph.</p>
*
--
GitLab
From 5080ce6473a829bcf90cb409540bee8d80eb650d Mon Sep 17 00:00:00 2001
From: LouisonF <fresnaislouison@gmail.com>
Date: Thu, 13 Oct 2022 18:13:18 +0200
Subject: [PATCH 8/8] Add write reaction main compounds
---
.../networkAnalysis/CarbonSkeletonNet.java | 86 ++++++++++++++-----
1 file changed, 63 insertions(+), 23 deletions(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
index 86807029e..0d20a766b 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/CarbonSkeletonNet.java
@@ -95,6 +95,9 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
@Option(name = "-ws", aliases = {"--writeReactionSideCompounds"}, usage = "export the list of reaction side compounds in a tabulated file", required = false)
public boolean writeReactionSideCompounds = false;
+
+ @Option(name = "-wm", aliases = {"--writeReactionMainCompounds"}, usage = "export the list of reaction main compounds in a tabulated file", required = false)
+ public boolean writeReactionMainCompounds = false;
@Option(name = "-i", aliases = {"--fromIndexes"}, usage = "Use GSAM output with carbon indexes", required = false)
public boolean fromIndexes = false;
@@ -207,6 +210,16 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
EdgeMerger.mergeEdgesWithOverride(graph);
System.out.println(" Done.");
}
+ //Save compoundgraph version before the reactiongraph phase
+ //export graph
+ System.out.print("Exporting...");
+ if (asMatrix) {
+ ComputeAdjacencyMatrix adjBuilder = new ComputeAdjacencyMatrix(graph);
+ if (!computeWeight) adjBuilder.parallelEdgeWeightsHandling((u, v) -> Math.max(u, v));
+ ExportMatrix.toCSV(this.outputPath, adjBuilder.getadjacencyMatrix());
+ } else {
+ ExportGraph.toGmlWithAttributes(graph,this.outputPath, true);
+ }
//get the reaction graph
if(reactiongraph){
@@ -223,9 +236,9 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
while ((currentLine = rscpsReader.readLine()) != null){
String[] splitLine = currentLine.split("\t");
BioCollection<BioMetabolite> scpsSet = new BioCollection<BioMetabolite>();
- for(String met : splitLine[1].replaceAll("[\\[\\]]", "").split(",")){
+ //TODO clean this
+ for(String met : splitLine[1].split(",")){
scpsSet.add(graph.getVertex(met));
- System.out.println(met);
}
reactionSideCompounds.put(ReactionMap.get(splitLine[0]), scpsSet);
}
@@ -237,15 +250,47 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
}
//If a globalSideCompounds file is provided
if(!Objects.isNull(globalSideCompoundsFile)){
- //read content of file
NodeMapping<BioMetabolite, ReactionEdge, CompoundGraph> mapper = new NodeMapping<>(graph).skipIfNotFound();
BioCollection<BioMetabolite> sideCpds = mapper.map(globalSideCompoundsFile);
- rgraph = builder.getReactionGraph(reactionSideCompounds,sideCpds);
+ // rgraph = builder.getReactionGraph(reactionSideCompounds,sideCpds);
+ rgraph = builder.getSimplifiedReactionGraph(reactionSideCompounds,sideCpds);
}else{
rgraph = builder.getReactionGraph(reactionSideCompounds);
}
ExportGraph.toGmlWithAttributes(rgraph, "reactiongraph_"+this.outputPath, true);
}
+ //write reaction main compounds
+ if(writeReactionMainCompounds){
+ RPAIRSlikePolicy rp = new RPAIRSlikePolicy(wp);
+ rp.setWeight(graph);
+ HashMap<BioReaction,BioCollection<BioMetabolite>> reactionMainCompounds = rp.getReactionMainCompounds(graph);
+ BufferedWriter fw = new BufferedWriter(new FileWriter("reactionMCs_"+outputPath.replace(".gml", ".tab"),false),8*1024);
+ try{
+ fw.write("ReactionID\tMainCpds\n");
+ for(BioReaction elem : reactionMainCompounds.keySet()){
+ //Instanciate iterator
+ try {
+ Iterator<BioMetabolite> it = reactionMainCompounds.get(elem).iterator();
+ fw.write(elem.getId()+"\t");
+ while(it.hasNext()){
+ String met = it.next().getId();
+ if(it.hasNext()){
+ fw.write(met+",");
+ }else{
+ fw.write(met);
+ }
+ }
+ fw.write("\n");
+ } catch (NullPointerException e) {
+ fw.write(elem.getId()+"\t"+"\n");
+ }
+
+ }
+ fw.close();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
//write reaction side compounds
if(writeReactionSideCompounds){
@@ -257,33 +302,28 @@ public class CarbonSkeletonNet extends AbstractMet4jApplication {
fw.write("ReactionID\tSideCpds\n");
for(BioReaction elem : reactionSideCompounds.keySet()){
//Instanciate iterator
- Iterator<BioMetabolite> it = reactionSideCompounds.get(elem).iterator();
- fw.write(elem.getId()+"\t");
- while(it.hasNext()){
- String met = it.next().getId();
- if(it.hasNext()){
- fw.write(met+",");
- }else{
- fw.write(met);
+ try {
+ Iterator<BioMetabolite> it = reactionSideCompounds.get(elem).iterator();
+ fw.write(elem.getId()+"\t");
+ while(it.hasNext()){
+ String met = it.next().getId();
+ if(it.hasNext()){
+ fw.write(met+",");
+ }else{
+ fw.write(met);
+ }
}
+ fw.write("\n");
+ } catch (NullPointerException e) {
+ fw.write(elem.getId()+"\t"+"\n");
}
- fw.write("\n");
+
}
fw.close();
} catch (FileNotFoundException e) {
e.printStackTrace();
}
}
-
- //export graph
- System.out.print("Exporting...");
- if (asMatrix) {
- ComputeAdjacencyMatrix adjBuilder = new ComputeAdjacencyMatrix(graph);
- if (!computeWeight) adjBuilder.parallelEdgeWeightsHandling((u, v) -> Math.max(u, v));
- ExportMatrix.toCSV(this.outputPath, adjBuilder.getadjacencyMatrix());
- } else {
- ExportGraph.toGmlWithAttributes(graph, this.outputPath, true);
- }
System.out.println(" Done.");
return;
}
--
GitLab