From 3923b042128a19cca2b3753bddfc925405bdd29b Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Wed, 31 Aug 2022 17:22:37 +0200
Subject: [PATCH 1/7] create apps to export degree and chemical similarity
weights for compound graphs
---
.../met4j_toolbox/generic/EdgeWeighting.java | 136 ++++++++++++++++++
.../ChemSimilarityWeighting.java | 47 ++++++
.../networkAnalysis/DegreeWeighting.java | 32 +++++
3 files changed, 215 insertions(+)
create mode 100644 met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
create mode 100644 met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
create mode 100644 met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
new file mode 100644
index 000000000..e40702f86
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
@@ -0,0 +1,136 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.generic;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.ReactionProbabilityWeight;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.WeightUtils;
+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.core.WeightingPolicy;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
+import fr.inrae.toulouse.metexplore.met4j_graph.io.Bionetwork2BioGraph;
+import fr.inrae.toulouse.metexplore.met4j_graph.io.NodeMapping;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
+import fr.inrae.toulouse.metexplore.met4j_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_toolbox.generic.annotations.EnumFormats;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.EnumParameterTypes;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.Format;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.annotations.ParameterType;
+import org.kohsuke.args4j.Option;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+public abstract class EdgeWeighting 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)
+ @Option(name = "-sc", usage = "input Side compound file", required = false)
+ public String inputSide = null;
+
+ @ParameterType(name= EnumParameterTypes.OutputFile)
+ @Option(name = "-o", usage = "output edge weight 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 = "-me", aliases = {"--simple"}, usage = "merge parallel edges to produce a simple graph", required = false)
+ public boolean mergeEdges = false;
+
+ @Option(name = "-un", aliases = {"--undirected"}, usage = "create as undirected", required = false)
+ public boolean undirected = false;
+
+ @Option(name = "-tp", aliases = {"--transitionproba"}, usage = "set weight as random walk transition probability, normalized by reaction", required = false)
+ public boolean computeWeight = false;
+
+ @Option(name = "-nan", aliases = {"--removeNaN"}, usage = "do not output edges with undefined weight", required = false)
+ public boolean removeNaN = false;
+
+
+ public abstract WeightingPolicy setWeightingPolicy();
+
+ public void run() throws IOException, Met4jSbmlReaderException {
+
+ WeightingPolicy wp = setWeightingPolicy();
+
+ 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 = reader.read(pkgs);
+ System.out.println(" Done.");
+
+
+ System.out.print("Buildinig Network...");
+ Bionetwork2BioGraph builder = new Bionetwork2BioGraph(network);
+ CompoundGraph graph = builder.getCompoundGraph();
+ System.out.println(" Done.");
+
+ //Graph processing: side compound removal [optional]
+ if (inputSide != null) {
+ System.err.println("removing side compounds...");
+ NodeMapping<BioMetabolite, ReactionEdge, CompoundGraph> mapper = new NodeMapping<>(graph).skipIfNotFound();
+ BioCollection<BioMetabolite> sideCpds = mapper.map(inputSide);
+ boolean removed = graph.removeAllVertices(sideCpds);
+ if (removed) System.err.println(sideCpds.size() + " compounds removed.");
+ }
+
+ //Graph processing: set weights [optional]
+ wp.setWeight(graph);
+ if(removeNaN) WeightUtils.removeEdgeWithNaNWeight(graph);
+
+ //invert graph as undirected (copy edge weight to reversed edge)
+ if(undirected){
+ System.out.print("Create Undirected...");
+ graph.asUndirected();
+ System.out.println(" Done.");
+ }
+
+ //merge compartment
+ if(mergingStrat!= strategy.no){
+ System.out.print("Merging compartments...");
+ VertexContraction vc = new VertexContraction();
+ VertexContraction.Mapper merger = mergingStrat.equals(strategy.by_name) ? new VertexContraction.MapByName() : new VertexContraction.MapByIdSubString(idRegex);
+ graph = vc.decompartmentalize(graph, merger);
+ System.out.println(" Done.");
+ }
+
+ //compute transitions probability from weights
+ if(computeWeight) {
+ System.out.print("Compute transition matrix...");
+ ReactionProbabilityWeight wp2 = new ReactionProbabilityWeight();
+ wp2.setWeight(graph);
+ System.out.println(" Done.");
+ }
+
+ //merge parallel edges
+ if(mergeEdges){
+ System.out.print("Merging edges...");
+ EdgeMerger.mergeEdgesWithOverride(graph);
+ System.out.println(" Done.");
+ }
+
+ //export graph
+ System.out.print("Exporting...");
+ WeightUtils.export(graph,outputPath);
+ System.out.println(" Done.");
+ return;
+ }
+
+}
+
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
new file mode 100644
index 000000000..992306c91
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
@@ -0,0 +1,47 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
+
+import fr.inrae.toulouse.metexplore.met4j_chemUtils.chemicalSimilarity.FingerprintBuilder;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.SimilarityWeightPolicy;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.EdgeWeighting;
+import org.kohsuke.args4j.Option;
+
+public class ChemSimilarityWeighting extends EdgeWeighting {
+
+ enum strategy {EState,Extended,KlekotaRoth,MACCS,PubChem};
+ @Option(name = "-f", aliases = {"--fingerprint"}, usage = "The chemical fingerprint to use", required = false)
+ public strategy type = strategy.Extended;
+
+ @Option(name = "-d", aliases = {"--asDist"}, usage = "Use distance rather than similarity", required = false)
+ public boolean dist = false;
+ @Override
+
+
+ public WeightingPolicy setWeightingPolicy() {
+ SimilarityWeightPolicy wp = new SimilarityWeightPolicy();
+ switch(type){
+ case EState: wp.setFingerprintType(FingerprintBuilder.ESTATE);
+ case Extended: wp.setFingerprintType(FingerprintBuilder.EXTENDED);
+ case KlekotaRoth: wp.setFingerprintType(FingerprintBuilder.KLEKOTAROTH);
+ case MACCS: wp.setFingerprintType(FingerprintBuilder.MACCS);
+ case PubChem: wp.setFingerprintType(FingerprintBuilder.PUBCHEM);
+ }
+ wp.useDistance(dist);
+ return wp;
+ }
+
+ @Override
+ public String getLabel() {
+ return null;
+ }
+
+ @Override
+ public String getLongDescription() {
+ return null;
+ }
+
+ @Override
+ public String getShortDescription() {
+ return null;
+ }
+}
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
new file mode 100644
index 000000000..b4a0f56bd
--- /dev/null
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
@@ -0,0 +1,32 @@
+package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
+
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.DegreeWeightPolicy;
+import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
+import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.EdgeWeighting;
+import org.kohsuke.args4j.Option;
+
+public class DegreeWeighting extends EdgeWeighting {
+
+ @Option(name = "-pow", aliases = {"--power"}, usage = "set weights as the degree raised to the power of number in parameter.", required = false)
+ public int pow = 1;
+ @Override
+ public WeightingPolicy setWeightingPolicy() {
+ DegreeWeightPolicy wp = new DegreeWeightPolicy(pow);
+ return wp;
+ }
+
+ @Override
+ public String getLabel() {
+ return null;
+ }
+
+ @Override
+ public String getLongDescription() {
+ return null;
+ }
+
+ @Override
+ public String getShortDescription() {
+ return null;
+ }
+}
--
GitLab
From 8b6b1cd9a99618f9b50045545325db2f4b8fa784 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Wed, 21 Sep 2022 10:23:38 +0200
Subject: [PATCH 2/7] add App description and javadoc
---
.../met4j_toolbox/generic/EdgeWeighting.java | 3 +++
.../networkAnalysis/ChemSimilarityWeighting.java | 12 +++++++++---
.../networkAnalysis/DegreeWeighting.java | 12 +++++++++---
3 files changed, 21 insertions(+), 6 deletions(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
index e40702f86..f5742b724 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
@@ -28,6 +28,9 @@ import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
+/**
+ * Abstract class for app that provides tabulated compound graph edge list, with one column with edge weight.
+ */
public abstract class EdgeWeighting extends AbstractMet4jApplication {
@Format(name= EnumFormats.Sbml)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
index 992306c91..e3622cba2 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
@@ -6,6 +6,9 @@ import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.EdgeWeighting;
import org.kohsuke.args4j.Option;
+/**
+ * App that provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity
+ */
public class ChemSimilarityWeighting extends EdgeWeighting {
enum strategy {EState,Extended,KlekotaRoth,MACCS,PubChem};
@@ -32,16 +35,19 @@ public class ChemSimilarityWeighting extends EdgeWeighting {
@Override
public String getLabel() {
- return null;
+ return this.getClass().getSimpleName();
}
@Override
public String getLongDescription() {
- return null;
+ return "Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity." +
+ "Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks," +
+ " using shortest (lightest) path search. See McSha et al. 2003 (https://doi.org/10.1093/bioinformatics/btg217)," +
+ " Rahman et al. 2005 (https://doi.org/10.1093/bioinformatics/bti116) and Pertusi et al. 2014 (https://doi.org/10.1093/bioinformatics/btu760)";
}
@Override
public String getShortDescription() {
- return null;
+ return "Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.";
}
}
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
index b4a0f56bd..3ec24534a 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
@@ -5,6 +5,9 @@ import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.EdgeWeighting;
import org.kohsuke.args4j.Option;
+/**
+ * App that provides tabulated compound graph edge list, with one column with target's degree.
+ */
public class DegreeWeighting extends EdgeWeighting {
@Option(name = "-pow", aliases = {"--power"}, usage = "set weights as the degree raised to the power of number in parameter.", required = false)
@@ -17,16 +20,19 @@ public class DegreeWeighting extends EdgeWeighting {
@Override
public String getLabel() {
- return null;
+ return this.getClass().getSimpleName();
}
@Override
public String getLongDescription() {
- return null;
+ return "Provides tabulated compound graph edge list, with one column with target's degree." +
+ "Degree has been proposed as edge weight for finding meaningful paths in metabolic networks," +
+ " using shortest (lightest) path search. See Croes et al. 2006 (https://doi.org/10.1016/j.jmb.2005.09.079) and" +
+ " Croes et al. 2005 (https://doi.org/10.1093/nar/gki437)";
}
@Override
public String getShortDescription() {
- return null;
+ return "Provides tabulated compound graph edge list, with one column with target's degree.";
}
}
--
GitLab
From 98fd83d44f7ea1cc436c2291f81bd372bbdc458e Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 22 Sep 2022 15:03:08 +0200
Subject: [PATCH 3/7] [mapping] Add attribute mapping in Mapper class
---
.../metexplore/met4j_mapping/Mapper.java | 28 ++++++++++++++++-
.../metexplore/met4j_mapping/MapperTest.java | 30 +++++++++++++++++++
2 files changed, 57 insertions(+), 1 deletion(-)
diff --git a/met4j-mapping/src/main/java/fr/inrae/toulouse/metexplore/met4j_mapping/Mapper.java b/met4j-mapping/src/main/java/fr/inrae/toulouse/metexplore/met4j_mapping/Mapper.java
index 884ccb615..e41c4e390 100644
--- a/met4j-mapping/src/main/java/fr/inrae/toulouse/metexplore/met4j_mapping/Mapper.java
+++ b/met4j-mapping/src/main/java/fr/inrae/toulouse/metexplore/met4j_mapping/Mapper.java
@@ -43,7 +43,7 @@ import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
-import java.util.Collection;
+import java.util.*;
import java.util.function.Function;
import java.util.regex.Pattern;
@@ -145,6 +145,32 @@ public class Mapper<E extends BioEntity> {
return mapping;
}
+ /**
+ * From a tabulated file with one entity identifiers column and attributes columns, return a map with the corresponding entities instances found in the network as value
+ * and a list of attributes as value.
+ * @param reader the input stream holding identifiers
+ * @return a collection of matching entities
+ * @throws IOException
+ */
+ public Map<E, List<String>> mapAttributes(Reader reader) throws IOException {
+ this.skipped =0;
+ BufferedReader breader = new BufferedReader(reader);
+ HashMap<E, List<String>> mapping = new HashMap<>();
+ String line;
+ if(skipHeader) breader.readLine();
+ while ((line = breader.readLine()) != null) {
+ ArrayList<String> parsedLine = new ArrayList<String>(Arrays.asList(line.trim().split(sep)));
+ String id = parsedLine.get(col-1);
+ parsedLine.remove(col-1);
+ E e = this.get(id);
+ if(e!=null){
+ mapping.put(e,parsedLine);
+ }
+ }
+ breader.close();
+ return mapping;
+ }
+
public int getNumberOfSkippedEntries(){
return this.skipped;
}
diff --git a/met4j-mapping/src/test/java/fr/inrae/toulouse/metexplore/met4j_mapping/MapperTest.java b/met4j-mapping/src/test/java/fr/inrae/toulouse/metexplore/met4j_mapping/MapperTest.java
index f8ed1a37b..771649669 100644
--- a/met4j-mapping/src/test/java/fr/inrae/toulouse/metexplore/met4j_mapping/MapperTest.java
+++ b/met4j-mapping/src/test/java/fr/inrae/toulouse/metexplore/met4j_mapping/MapperTest.java
@@ -12,6 +12,7 @@ import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
import static org.junit.Assert.*;
@@ -97,6 +98,35 @@ public class MapperTest {
}
}
+ @Test
+ public void testMapper22(){
+ Mapper<BioMetabolite> m = new Mapper<>(bn, BioNetwork::getMetabolitesView)
+ .columnSeparator("\t")
+ .idColumn(2)
+ .skipHeader()
+ .skipIfNotFound();
+ try {
+ Map<BioMetabolite,List<String>> res = m.mapAttributes(r1);
+ assertEquals("wrong number of mapped entries", 3, res.size());
+ assertEquals("wrong number of skipped entries", 1, m.getNumberOfSkippedEntries());
+ assertTrue("reaction in file not found", res.keySet().contains(a));
+ assertTrue("reaction in file not found", res.keySet().contains(b));
+ assertTrue("reaction in file not found", res.keySet().contains(c));
+ assertEquals("Wrong number of attributes", 2,res.get(a).size());
+ assertEquals("Wrong number of attributes", 2,res.get(b).size());
+ assertEquals("Wrong number of attributes", 2,res.get(c).size());
+ assertEquals("Wrong attribute value", "A",res.get(a).get(0));
+ assertEquals("Wrong attribute value", "0.1",res.get(a).get(1));
+ assertEquals("Wrong attribute value", "B",res.get(b).get(0));
+ assertEquals("Wrong attribute value", "0.2",res.get(b).get(1));
+ assertEquals("Wrong attribute value", "C",res.get(c).get(0));
+ assertEquals("Wrong attribute value", "0.3",res.get(c).get(1));
+ } catch (IOException e) {
+ Assert.fail("mapping failed");
+ e.printStackTrace();
+ }
+ }
+
@Test
public void testMapper3(){
Mapper<BioReaction> m = new Mapper<>(bn, BioNetwork::getReactionsView).skipIfNotFound();
--
GitLab
From 73150b1db1d364d606d07cf247d9466fddd5c0bf Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 22 Sep 2022 15:04:05 +0200
Subject: [PATCH 4/7] add optional processing in Abstract weighting app
---
.../met4j_toolbox/generic/EdgeWeighting.java | 20 +++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
index f5742b724..1cc13fb4a 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/generic/EdgeWeighting.java
@@ -76,12 +76,14 @@ public abstract class EdgeWeighting extends AbstractMet4jApplication {
ArrayList<PackageParser> pkgs = new ArrayList<>(Arrays.asList(
new NotesParser(false), new FBCParser(), new GroupPathwayParser()));
BioNetwork network = reader.read(pkgs);
+ network = processNetwork(network);
System.out.println(" Done.");
System.out.print("Buildinig Network...");
Bionetwork2BioGraph builder = new Bionetwork2BioGraph(network);
CompoundGraph graph = builder.getCompoundGraph();
+ graph = processCompoundGraph(graph);
System.out.println(" Done.");
//Graph processing: side compound removal [optional]
@@ -135,5 +137,23 @@ public abstract class EdgeWeighting extends AbstractMet4jApplication {
return;
}
+ /**
+ * Methods to add optional preprocessing of the compound graph
+ * @param graph the original compound graph
+ * @return a preprocessed graph
+ */
+ public CompoundGraph processCompoundGraph(CompoundGraph graph) {
+ return graph;
+ }
+
+ /**
+ * Methods to add optional preprocessing of SBML parsing output
+ * @param network the original network from parsed SBML
+ * @return a preprocessed network
+ */
+ public BioNetwork processNetwork(BioNetwork network) {
+ return network;
+ }
+
}
--
GitLab
From da89456f6070f65bc6abdfb658e054fa9ce145c9 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 22 Sep 2022 15:04:40 +0200
Subject: [PATCH 5/7] add missing main + add SMILE/INCHI import in chemical
similarity weighting
---
.../ChemSimilarityWeighting.java | 62 ++++++++++++++++++-
.../networkAnalysis/DegreeWeighting.java | 14 +++++
2 files changed, 74 insertions(+), 2 deletions(-)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
index e3622cba2..42e5abc50 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
@@ -1,11 +1,21 @@
package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
import fr.inrae.toulouse.metexplore.met4j_chemUtils.chemicalSimilarity.FingerprintBuilder;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.SimilarityWeightPolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
+import fr.inrae.toulouse.metexplore.met4j_mapping.Mapper;
import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.EdgeWeighting;
import org.kohsuke.args4j.Option;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
/**
* App that provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity
*/
@@ -15,11 +25,15 @@ public class ChemSimilarityWeighting extends EdgeWeighting {
@Option(name = "-f", aliases = {"--fingerprint"}, usage = "The chemical fingerprint to use", required = false)
public strategy type = strategy.Extended;
+ @Option(name = "-sm", aliases = {"--smileFile"}, usage = "If not present in SBML's annotations, get structure from a tabulated file with first column as compound id and second column as SMILE string, no header. Ignored if inchi file is provided", required = false)
+ public String smileFile;
+ @Option(name = "-in", aliases = {"--inchiFile"}, usage = "If not present in SBML's annotations, get structure from a tabulated file with first column as compound id and second column as InChI string, no header.", required = false)
+ public String inchiFile;
+
@Option(name = "-d", aliases = {"--asDist"}, usage = "Use distance rather than similarity", required = false)
public boolean dist = false;
- @Override
-
+ @Override
public WeightingPolicy setWeightingPolicy() {
SimilarityWeightPolicy wp = new SimilarityWeightPolicy();
switch(type){
@@ -33,6 +47,50 @@ public class ChemSimilarityWeighting extends EdgeWeighting {
return wp;
}
+ @Override
+ public BioNetwork processNetwork(BioNetwork bn){
+ if(inchiFile!=null){
+ Mapper m = new Mapper<>(bn, BioNetwork::getMetabolitesView)
+ .columnSeparator("\t")
+ .idColumn(1)
+ .skipIfNotFound();
+ try {
+ Map<BioMetabolite, List<String>> att = m.mapAttributes(new BufferedReader(new FileReader(inchiFile)));
+ for(Map.Entry<BioMetabolite, List<String>> entry : att.entrySet()){
+ entry.getKey().setInchi(entry.getValue().get(0));
+ }
+ } catch (IOException e) {
+ System.err.println("Error reading InChI file");
+ throw new RuntimeException(e);
+ }
+ } else if (smileFile!=null) {
+ Mapper m = new Mapper<>(bn, BioNetwork::getMetabolitesView)
+ .columnSeparator("\t")
+ .idColumn(1)
+ .skipIfNotFound();
+ try {
+ Map<BioMetabolite, List<String>> att = m.mapAttributes(new BufferedReader(new FileReader(smileFile)));
+ for(Map.Entry<BioMetabolite, List<String>> entry : att.entrySet()){
+ entry.getKey().setSmiles(entry.getValue().get(0));
+ }
+ } catch (IOException e) {
+ System.err.println("Error reading InChI file");
+ throw new RuntimeException(e);
+ }
+ }
+ return bn;
+ }
+
+ public static void main(String[] args) throws Met4jSbmlReaderException, IOException {
+
+ ChemSimilarityWeighting app = new ChemSimilarityWeighting();
+
+ app.parseArguments(args);
+
+ app.run();
+
+ }
+
@Override
public String getLabel() {
return this.getClass().getSimpleName();
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
index 3ec24534a..a55cb91bd 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/DegreeWeighting.java
@@ -2,9 +2,12 @@ package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.DegreeWeightPolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.EdgeWeighting;
import org.kohsuke.args4j.Option;
+import java.io.IOException;
+
/**
* App that provides tabulated compound graph edge list, with one column with target's degree.
*/
@@ -12,12 +15,23 @@ public class DegreeWeighting extends EdgeWeighting {
@Option(name = "-pow", aliases = {"--power"}, usage = "set weights as the degree raised to the power of number in parameter.", required = false)
public int pow = 1;
+
@Override
public WeightingPolicy setWeightingPolicy() {
DegreeWeightPolicy wp = new DegreeWeightPolicy(pow);
return wp;
}
+ public static void main(String[] args) throws Met4jSbmlReaderException, IOException {
+
+ DegreeWeighting app = new DegreeWeighting();
+
+ app.parseArguments(args);
+
+ app.run();
+
+ }
+
@Override
public String getLabel() {
return this.getClass().getSimpleName();
--
GitLab
From b63f6a536bdbd1350d362b3d5ed41f3c778eee49 Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 22 Sep 2022 15:29:24 +0200
Subject: [PATCH 6/7] add check for missing chemical structure in
chemsimilarity
---
.../networkAnalysis/ChemSimilarityWeighting.java | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
index 42e5abc50..5b1566593 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ChemSimilarityWeighting.java
@@ -3,6 +3,7 @@ package fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis;
import fr.inrae.toulouse.metexplore.met4j_chemUtils.chemicalSimilarity.FingerprintBuilder;
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.utils.StringUtils;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.SimilarityWeightPolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
@@ -78,6 +79,18 @@ public class ChemSimilarityWeighting extends EdgeWeighting {
throw new RuntimeException(e);
}
}
+ int s = 0;
+ int i = 0;
+ for(BioMetabolite m : bn.getMetabolitesView()){
+ if(!StringUtils.isVoid(m.getSmiles())) s++;
+ if(!StringUtils.isVoid(m.getInchi())) i++;
+ }
+ System.out.println(s+"/"+bn.getMetabolitesView().size()+" metabolites with SMILE");
+ System.out.println(i+"/"+bn.getMetabolitesView().size()+" metabolites with InChI");
+ if((i+s)==0){
+ System.err.println("Error: no chemical structure provided, unable to compute chemical similarity");
+ System.exit(1);
+ }
return bn;
}
--
GitLab
From 36967fd22bcc34cd024cd37504accae7dfc82d9c Mon Sep 17 00:00:00 2001
From: cfrainay <clement.frainay@inrae.fr>
Date: Thu, 22 Sep 2022 15:31:01 +0200
Subject: [PATCH 7/7] update changelog
---
CHANGELOG.md | 1 +
1 file changed, 1 insertion(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d7af514b8..66361e8d9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Features
+[met4j-toolbox] Add Apps to compute compound graph's classical weights (degree/chemical similarity)
[met4j-graph] Add method to create RPAIRs-like tags on compound graph's edges
--
GitLab