TC family identifier | search by taxonomy fixed

src/main/java/biosynth/BuildDatabase.java

@@ -5,7 +5,10 @@ import org.neo4j.graphdb.GraphDatabaseService;
 import edu.uminho.biosynth.core.data.integration.neo4j.HelperNeo4jConfigInitializer;
 import pt.uminho.sysbio.biosynth.integration.GraphMetaboliteEntity;
 import pt.uminho.sysbio.biosynth.integration.etl.EtlTransform;
+import pt.uminho.sysbio.biosynthframework.biodb.bigg.Bigg2MetaboliteEntity;
+import pt.uminho.sysbio.biosynthframework.biodb.bigg.BiggMetaboliteEntity;
 import pt.uminho.sysbio.biosynthframework.biodb.biocyc.BioCycMetaboliteEntity;
+import pt.uminho.sysbio.biosynthframework.biodb.seed.ModelSeedMetaboliteEntity;
 import pt.uminho.sysbio.biosynthframework.io.MetaboliteDao;
 
 public class BuildDatabase {
@@ -15,91 +18,91 @@ public class BuildDatabase {
 		System.out.println("setting GraphDatabaseService...");
 		
 		GraphDatabaseService graphDatabaseService = HelperNeo4jConfigInitializer
-				.initializeNeo4jDataDatabaseConstraints("C:\\Users\\Davide\\Documents\\BASE DE DADOS BIOSYNTH\\db3_0");
-		
-//		///////////////////////////////////////////////////////////
-//		System.out.println();
-//		System.out.println("requesting kegg compounds...");
-//		
-//		KEGG.etl(KEGG.getKeggCompoundMetaboliteDao() , KEGG.getKeggCompoundTransform(), graphDatabaseService);
-//		
-//		System.out.println("requesting kegg glycans...");
-//		
-//		KEGG.etl(KEGG.getKeggGlycanMetaboliteDao() , KEGG.getKeggGlycanTransform(), graphDatabaseService);	
-//		
-//		///////////////////////////////////////////////////////////
-//		
-//		System.out.println();
-//		System.out.println("opening BIGG1...");
-//		
-//		EtlTransform<BiggMetaboliteEntity, GraphMetaboliteEntity> t1 = BIGG1.getBiggMetaboliteTransform();
-//		
-//		MetaboliteDao<BiggMetaboliteEntity> daoBigg1 = BIGG1.getBigg1MetaboliteDatabase();
-//		
-//		System.out.println("transforming...");
-//		
-//		BIGG1.etl(daoBigg1, t1, graphDatabaseService);
-//
-//		System.out.println("BIGG1 complete...");
-//		
-//		///////////////////////////////////////////////////////////
-//		System.out.println();
-//		System.out.println("opening BIGG2...");
-//		
-//		EtlTransform<Bigg2MetaboliteEntity, GraphMetaboliteEntity> t2 = BIGG2.getBIGG2MetaboliteTransform();
-//		MetaboliteDao<Bigg2MetaboliteEntity> daoBigg2 = BIGG2.getBigg2MetaboliteDao();
-//		
-//		System.out.println("transforming...");
-//		
-//		BIGG2.etl(daoBigg2 , t2, graphDatabaseService);
-//		
-//		System.out.println("BIGG2 complete...");
-//		
-//		///////////////////////////////////////////////////////////
-//		System.out.println();
-//		System.out.println("opening Metacyc META...");
-//		
-//		EtlTransform<BioCycMetaboliteEntity, GraphMetaboliteEntity> t3 = Metacyc.getMetacycMetaboliteTransform();
-////		MetaboliteDao<BiggMetaboliteEntity> daoBigg = getBigg1MetaboliteDatabase();
-//		MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc3 = Metacyc.getMetacycMetaboliteDao("META");
-//		
-//		System.out.println("transforming...");
-//		
-//		Metacyc.etl(daoBiocyc3 , t3, graphDatabaseService);
-//		
-//		System.out.println("Metacyc META complete...");
-//		
-//		///////////////////////////////////////////////////////////
-//		System.out.println();
-		
-//		System.out.println("opening Metacyc ECOLI...");
-//		
-//		EtlTransform<BioCycMetaboliteEntity, GraphMetaboliteEntity> t4 = Metacyc.getMetacycMetaboliteTransform();
-//		MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc4 = Metacyc.getMetacycMetaboliteDao("ECOLI");
-//		
-//		System.out.println("transforming...");
-//		
-//		Metacyc.etl(daoBiocyc4 , t4, graphDatabaseService);
-//		
-//		System.out.println("Metacyc ECOLI complete...");
+				.initializeNeo4jDataDatabaseConstraints("C:\\Users\\Davide\\Documents\\BASE DE DADOS BIOSYNTH\\db5_0");
+		
+		///////////////////////////////////////////////////////////
+		System.out.println();
+		System.out.println("requesting kegg compounds...");
+		
+		KEGG.etl(KEGG.getKeggCompoundMetaboliteDao() , KEGG.getKeggCompoundTransform(), graphDatabaseService);
+		
+		System.out.println("requesting kegg glycans...");
+		
+		KEGG.etl(KEGG.getKeggGlycanMetaboliteDao() , KEGG.getKeggGlycanTransform(), graphDatabaseService);	
+		
+		///////////////////////////////////////////////////////////
+		
+		System.out.println();
+		System.out.println("opening BIGG1...");
+		
+		EtlTransform<BiggMetaboliteEntity, GraphMetaboliteEntity> t1 = BIGG1.getBiggMetaboliteTransform();
+		
+		MetaboliteDao<BiggMetaboliteEntity> daoBigg1 = BIGG1.getBigg1MetaboliteDatabase();
+		
+		System.out.println("transforming...");
+		
+		BIGG1.etl(daoBigg1, t1, graphDatabaseService);
+
+		System.out.println("BIGG1 complete...");
+		
+		///////////////////////////////////////////////////////////
+		System.out.println();
+		System.out.println("opening BIGG2...");
+		
+		EtlTransform<Bigg2MetaboliteEntity, GraphMetaboliteEntity> t2 = BIGG2.getBIGG2MetaboliteTransform();
+		MetaboliteDao<Bigg2MetaboliteEntity> daoBigg2 = BIGG2.getBigg2MetaboliteDao();
+		
+		System.out.println("transforming...");
+		
+		BIGG2.etl(daoBigg2 , t2, graphDatabaseService);
+		
+		System.out.println("BIGG2 complete...");
+		
+		///////////////////////////////////////////////////////////
+		System.out.println();
+		System.out.println("opening Metacyc META...");
+		
+		EtlTransform<BioCycMetaboliteEntity, GraphMetaboliteEntity> t3 = Metacyc.getMetacycMetaboliteTransform();
+//		MetaboliteDao<BiggMetaboliteEntity> daoBigg = getBigg1MetaboliteDatabase();
+		MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc3 = Metacyc.getMetacycMetaboliteDao("META");
+		
+		System.out.println("transforming...");
+		
+		Metacyc.etl(daoBiocyc3 , t3, graphDatabaseService);
+		
+		System.out.println("Metacyc META complete...");
+		
+		///////////////////////////////////////////////////////////
+		System.out.println();
+		
+		System.out.println("opening Metacyc ECOLI...");
+		
+		EtlTransform<BioCycMetaboliteEntity, GraphMetaboliteEntity> t4 = Metacyc.getMetacycMetaboliteTransform();
+		MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc4 = Metacyc.getMetacycMetaboliteDao("ECOLI");
+		
+		System.out.println("transforming...");
+		
+		Metacyc.etl(daoBiocyc4 , t4, graphDatabaseService);
+		
+		System.out.println("Metacyc ECOLI complete...");
 		//////////////////////////////////////////////
 		
-//		System.out.println("opening ModelSEED...");
-//		
-//		EtlTransform<ModelSeedMetaboliteEntity, GraphMetaboliteEntity> t0 = ModelSEED.getMetaboliteTransform();
-//		
-//		MetaboliteDao<ModelSeedMetaboliteEntity> dao0 = ModelSEED.getMetaboliteDatabase();
-//		
-//		System.out.println("transforming...");
-//		
-//		ModelSEED.etl(dao0 , t0, graphDatabaseService);
-//		
-//		System.out.println("ModelSEED complete...");
-//		
+		System.out.println("opening ModelSEED...");
+		
+		EtlTransform<ModelSeedMetaboliteEntity, GraphMetaboliteEntity> t0 = ModelSEED.getMetaboliteTransform();
+		
+		MetaboliteDao<ModelSeedMetaboliteEntity> dao0 = ModelSEED.getMetaboliteDatabase();
+		
+		System.out.println("transforming...");
+		
+		ModelSEED.etl(dao0 , t0, graphDatabaseService);
+		
+		System.out.println("ModelSEED complete...");
+		
 		ModelSEED.createModelSEEDRelationships(graphDatabaseService);
 		
-//		System.out.println("database load complete...");
-//		
+		System.out.println("database load complete...");
+		
 		graphDatabaseService.shutdown();
 		
 		System.out.println("shutdown...");

src/main/java/biosynth/KEGG.java

@@ -84,7 +84,7 @@ public class KEGG {
 
 		HbmNeo4jHybridMetaboliteEtlPipeline<M, GraphMetaboliteEntity> etlPipeline =
 				new HbmNeo4jHybridMetaboliteEtlPipeline<>();
-		//		    etlPipeline.exclude.add("D05511");
+				    etlPipeline.exclude.add("D05511");
 		etlPipeline.setSkipLoad(false);
 		etlPipeline.setGraphDatabaseService(graphDatabaseService);
 		etlPipeline.setSessionFactory(null);

src/main/java/biosynth/ModelSEED.java

@@ -193,7 +193,7 @@ public class ModelSEED {
 					MetaboliteMajorLabel label = null;
 
 					if(source.equalsIgnoreCase("BiGG1"))
-						label = MetaboliteMajorLabel.BiGG2;
+						label = MetaboliteMajorLabel.BiGG;
 
 					else if(source.equalsIgnoreCase("KEGG")) {
 						label = MetaboliteMajorLabel.LigandCompound;
@@ -208,7 +208,7 @@ public class ModelSEED {
 					}
 
 					if(source.equalsIgnoreCase("BiGG"))
-						label = MetaboliteMajorLabel.BiGG;
+						label = MetaboliteMajorLabel.BiGGMetabolite;
 
 					if(label != null && !id.isEmpty() && !externalID.isEmpty()) {
 

src/main/java/internalDB/WriteByMetabolitesID.java

@@ -36,6 +36,7 @@ import uk.ac.ebi.chebi.webapps.chebiWS.model.LiteEntity;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.LiteEntityList;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.SearchCategory;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.StarsCategory;
+import utilities.triage_utilities.Properties;
 
 /**
  * @author Davide
@@ -48,6 +49,8 @@ public class WriteByMetabolitesID {
 	public static void main(String[] args) {
 		
 		try {
+			
+			Properties properties = new Properties();
 
 			GraphDatabaseService graphDatabaseService = initializeNeo4jdb.getDataDatabase(null);
 			Transaction dataTx = graphDatabaseService.beginTx();
@@ -93,7 +96,7 @@ public class WriteByMetabolitesID {
 				
 //				 new FetchCompoundsByName(service, false).getResults();	
 
-				test(namesAndIDsContainer, data, service, null, reactionsData, null);		//uncomment
+				test(namesAndIDsContainer, data, service, null, reactionsData, null, properties);		//uncomment
 
 //								test2(service);
 
@@ -169,19 +172,19 @@ public class WriteByMetabolitesID {
 
 
 	public static void test(BiosynthMetabolites namesAndIDsContainer, Map<String, BiosynthMetaboliteProperties> data, BiodbGraphDatabaseService service, Map<String, Map<String, MetaboliteMajorLabel>> tcdbMetabolitesIDs,
-			Map<String, Set<TcNumberContainer2>> reactionsData, Map<String, String[]> forChildsSearch) {
+			Map<String, Set<TcNumberContainer2>> reactionsData, Map<String, String[]> forChildsSearch, Properties properties) {
 
 //		 new FetchCompoundsByName(service, false).getResults();	
 		
 		try {
 			
-						Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>();
+//						Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>();
 
-						reactionsData2.put("P02916", reactionsData.get("P02916"));
+//						reactionsData2.put("P0A927", reactionsData.get("P0A927"));
 //						reactionsData2.put("P0AEE5", reactionsData.get("P0AEE5"));
 //						reactionsData2.put("P23200", reactionsData.get("P23200"));
 
-			IdentifyReactionsMetabolites metabolitesIdentification =  new IdentifyReactionsMetabolites(reactionsData2, namesAndIDsContainer, service);
+			IdentifyReactionsMetabolites metabolitesIdentification =  new IdentifyReactionsMetabolites(reactionsData, namesAndIDsContainer, service);
 
 			tcdbMetabolitesIDs = metabolitesIdentification.getTcdbMetabolitesIDs();
 
@@ -191,27 +194,32 @@ public class WriteByMetabolitesID {
 
 			//			reactionsData3.put("O51235", reactionsData.get("O51235"));
 			
-			System.out.println(tcdbMetabolitesIDs);
+//			System.out.println(tcdbMetabolitesIDs);
 
 			/////TRIAGE
-			Map<String, Set<TcNumberContainer2>> newData = new TransportReactionsBuilder(tcdbMetabolitesIDs, reactionsData2, forChildsSearch, service, data, namesAndIDsContainer.getMetabolitesIDs()).getResults();		//uncomment
+			Map<String, Set<TcNumberContainer2>> newData = new TransportReactionsBuilder(tcdbMetabolitesIDs, reactionsData, forChildsSearch, service, data, namesAndIDsContainer.getMetabolitesIDs(), properties).getResults();		//uncomment
 
 //			System.out.println(service.getNodeById(Long.valueOf(65729)).getAllProperties());
 			
-			for(TcNumberContainer2 container : newData.get("P02916")) {
-				
-				System.out.println(container.getTcNumber());
-				
-				for( Integer id : container.getAllReactionsIds()) {
-					System.out.println();
-					System.out.println(container.getReactionContainer(id).getReaction());
-					System.out.println(container.getReactionContainer(id).getReactionMetaCyc());
-					System.out.println(container.getReactionContainer(id).getReactionModelSEED());
-				}
-				
-				
-				System.out.println();
-			}
+//			for(TcNumberContainer2 container : newData.get("P0A927")) {
+//				
+//				System.out.println(container.getTcNumber());
+//				
+//				for( Integer id : container.getAllReactionsIds()) {
+//					System.out.println();
+//					
+//					System.out.println(container.getReactionContainer(id).getReactionID());
+//					System.out.println(container.getReactionContainer(id).getReaction());
+//					System.out.println(container.getReactionContainer(id).getReactionBase());
+//					System.out.println(container.getReactionContainer(id).getReactionKEGG());
+//					System.out.println(container.getReactionContainer(id).getReactionBiGG());
+//					System.out.println(container.getReactionContainer(id).getReactionMetaCyc());
+//					System.out.println(container.getReactionContainer(id).getReactionModelSEED());
+//				}
+//				
+//				
+//				System.out.println();
+//			}
 			
 			
 			

src/main/java/kbase/Reports.java

@@ -110,7 +110,7 @@ public class Reports {
 
 				JSONObject obj2 = new JSONObject();
 
-				String tcFamily = getFamilyForAnnotation(container);
+				String tcFamily = "";
 
 				if(!tcFamily.equals("none"))
 					totalGenesAnnotated++;
@@ -211,7 +211,7 @@ public class Reports {
 	 * @param container
 	 * @return
 	 */
-	private static String getFamilyForAnnotation(Map<String, Set<String>> container) { 
+	public static String getFamilyForAnnotation(Map<String, Set<String>> container) { 
 		Map<String, Integer> counts = new HashMap<>();
 
 		int maxCount = 0;
@@ -221,7 +221,12 @@ public class Reports {
 
 			String[] split = tc.split("\\.");
 
-			tc = split[0].concat(".").concat(split[1]).concat(".").concat(split[2]).concat(".");
+			try {
+				tc = split[0].concat(".").concat(split[1]).concat(".").concat(split[2]).concat(".");
+			} 
+			catch (Exception e) {
+				System.out.println("ERRO FAMILIA " + tc);
+			}
 
 			if(counts.containsKey(tc)) {
 
@@ -241,7 +246,7 @@ public class Reports {
 			}
 		}
 
-		return tcFamily.replaceAll("\\.$", "");
+		return tcFamily;
 	}
 
 }

src/main/java/reactions/IdentifyReactionsMetabolites.java

@@ -326,6 +326,9 @@ public class IdentifyReactionsMetabolites {
 
 		for(String metabolite : new HashSet<>(metabolites)) {
 			
+			if(metabolite.equalsIgnoreCase("galactonate"))
+				metabolite = "l-galactonate";
+			
 //			System.out.println(metabolite);
 //			
 //			System.out.println("map " + metabolite + "\t" + allMetabolitesByName.get(metabolite));
@@ -593,15 +596,15 @@ public class IdentifyReactionsMetabolites {
 				forChildsSearch.put(metabolite, entry);
 			}
 			
-			if(ids.containsKey(MetaboliteMajorLabel.MetaCyc))
+			if(ids.containsKey(MetaboliteMajorLabel.ModelSeed))
+				return MetaboliteMajorLabel.ModelSeed;
+			
+			else if(ids.containsKey(MetaboliteMajorLabel.MetaCyc))
 				return MetaboliteMajorLabel.MetaCyc;
 			
 			else if(ids.containsKey(MetaboliteMajorLabel.EcoCyc))
 				return MetaboliteMajorLabel.EcoCyc;
 
-			if(ids.containsKey(MetaboliteMajorLabel.ModelSeed))
-				return MetaboliteMajorLabel.ModelSeed;
-
 			else if(ids.containsKey(MetaboliteMajorLabel.LigandCompound))
 				return MetaboliteMajorLabel.LigandCompound;
 			

src/main/java/reactions/ProvideTransportReactionsToGenes.java

@@ -7,6 +7,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Scanner;
@@ -49,6 +50,7 @@ import pt.uminho.ceb.biosystems.mew.biocomponents.container.io.readers.JSBMLRead
 import pt.uminho.ceb.biosystems.mew.biocomponents.validation.io.JSBMLValidationException;
 import tcdb.capsules.GeneContainer;
 import tcdb.capsules.ReactionContainer;
+import tcdb.capsules.Subunits;
 import triageDatabase.TriageGeneralProperties;
 import triageDatabase.TriageGraphDatabaseService;
 import triageDatabase.TriageNeo4jInitializer;
@@ -87,6 +89,7 @@ public class ProvideTransportReactionsToGenes {
 	private Map<String, String> modelMetabolites;
 
 	private TriageGeneralProperties defaultLabel;
+	private Subunits subunits;
 
 	private static final Logger logger = LoggerFactory.getLogger(WriteByMetabolitesID.class);
 
@@ -106,12 +109,13 @@ public class ProvideTransportReactionsToGenes {
 		this.taxID = taxID;
 		this.jobIdentification = new File(queryPath).getName().replace(".faa", "");
 
+		subunits = new Subunits();
 		defaultLabel = getDefaultLabel();
 
 		findTaxonomyByTaxonomyID(taxID);
 
 		try {
-			Blast blast = new Blast(true, queryPath, properties);
+			Blast blast = new Blast(false, queryPath, properties);
 			blastResults = blast.getAlignmentsByQuery();
 
 			queryFileTotalOfGenes = blast.getQueryFileSize();
@@ -133,7 +137,7 @@ public class ProvideTransportReactionsToGenes {
 			while (n != 99) {
 
 
-				//										tests();
+//				tests();
 
 				start();	//uncomment
 
@@ -163,35 +167,70 @@ public class ProvideTransportReactionsToGenes {
 	}
 
 	private void tests() {
-
-		String tc = "3.D.1.1.1";
-
-		Node tcNumberNode = service.findTcNumberNode(tc);
-
-		System.out.println(tc);
-
-		System.out.println("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!");
-
-		if(tcNumberNode != null) {
-
-			System.out.println(tcNumberNode.getAllProperties());
-
-			Iterable<Relationship> relations = tcNumberNode.getRelationships(TriageRelationshipType.has_reaction);
-
-			for(Relationship rel : relations) {
-
-				System.out.println(rel.getEndNode().getAllProperties());
-				System.out.println(rel.getEndNode().getProperty("ReactionID") + "\t********\t" + rel.getEndNode().getProperty("Reaction"));
-
-				if(rel.getEndNode().hasProperty(TriageGeneralProperties.ReactionModelSEED.toString()))
-
-					System.out.println(rel.getEndNode().getProperty("ReactionID") + "\t********\t" + rel.getEndNode().getProperty(TriageGeneralProperties.ReactionModelSEED.toString()));
-
+		
+		
+		try {
+			Set<Node> list = service.getAllNodesByLabel(TriageNodeLabel.Reaction);
+		
+			Iterator<Node> iterator = list.iterator();
+		
+			Set<String> metabolites = new HashSet<>();
+			
+			while(iterator.hasNext()) {
+				
+				Node node = iterator.next();
+				
+				String reaction = node.getProperty(TriageGeneralProperties.ReactionBase.toString()).toString();
+				
+				boolean reversible = Boolean.valueOf(node.getProperty(TriageGeneralProperties.Reversible.toString()).toString());
+				
+				String regex = ReactionContainer.IRREV_TOKEN;
+				
+				if(reversible)
+					regex = ReactionContainer.REV_TOKEN;
+				
+				String[] compounds = reaction.replaceAll(regex, " + ").split("\\s+\\+\\s+");
+				
+				for(String c : compounds)
+					metabolites.add(c.replaceAll("=ModelSeed", "").replaceAll("\\(in\\)", "").replaceAll("\\(out\\)", "").trim());
+				
 			}
-
+			
+			System.out.println(metabolites.size());
+		} 
+		catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
 		}
-		else
-			System.out.println("nulo");
+
+//		String tc = "3.D.1.1.1";
+//
+//		Node tcNumberNode = service.findTcNumberNode(tc);
+//
+//		System.out.println(tc);
+//
+//		System.out.println("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!");
+//
+//		if(tcNumberNode != null) {
+//
+//			System.out.println(tcNumberNode.getAllProperties());
+//
+//			Iterable<Relationship> relations = tcNumberNode.getRelationships(TriageRelationshipType.has_reaction);
+//
+//			for(Relationship rel : relations) {
+//
+//				System.out.println(rel.getEndNode().getAllProperties());
+//				System.out.println(rel.getEndNode().getProperty("ReactionID") + "\t********\t" + rel.getEndNode().getProperty("Reaction"));
+//
+//				if(rel.getEndNode().hasProperty(TriageGeneralProperties.ReactionModelSEED.toString()))
+//
+//					System.out.println(rel.getEndNode().getProperty("ReactionID") + "\t********\t" + rel.getEndNode().getProperty(TriageGeneralProperties.ReactionModelSEED.toString()));
+//
+//			}
+//
+//		}
+//		else
+//			System.out.println("nulo");
 	}
 
 	private void findTaxonomyByTaxonomyID(Integer taxID) {
@@ -244,40 +283,52 @@ public class ProvideTransportReactionsToGenes {
 
 			logger.debug("Searching reactions...");
 
-			resultsByEvalue = ReactionsPredictor.getReactionsForGenesByEvalue(blastResults, properties.geteValueThreshold());
+			resultsByEvalue = getReactionsForGenesByEvalue();
+
+			Set<String> tcNumbers = identifyTcNumbersForSearch();
 
-			reactionsByTcNumber = getReactionsByTcNumber(identifyTcNumbersForSearch());
+			this.subunits.setSubunitsDatabase(findSubunitsInDatabase(tcNumbers));
+
+			reactionsByTcNumber = getReactionsByTcNumber(tcNumbers);
 
 			//			System.out.println(reactionsByTcNumber);
 
 			if(reactionContainersByID.keySet().size() == 0)
 				logger.warn("No metabolites present in the model are available in the selected reactions!");
 
-			Map<String, GeneContainer> data = buildGenesContainers();
+			Map<String, GeneContainer> genesContainers = buildGenesContainers();
 
-			Map<String, Map<String, Set<String>>> similaritiesResults = ReactionsPredictor.getReactionsForGenesBySimilarities(data, reactionsByTcNumber, blastResults, mainReactions, reactionsToIgnore);
+			Map<String, Set<String>> similaritiesResults = ReactionsPredictor.getReactionsForGenesBySimilarities(genesContainers, reactionsByTcNumber, blastResults, mainReactions, reactionsToIgnore);
 
 			String path = "C:\\Users\\Davide\\OneDrive - Universidade do Minho\\UMinho\\Tese\\KBase\\Reports\\ecoli_Validation30\\";
 
 			//			generateFinalResults(similaritiesResults);
-			generateFinalResultsAuxValidation(similaritiesResults, path);
+			generateFinalResultsAuxValidation(similaritiesResults, genesContainers, path);
 
 			//						System.out.println(finalResults);
 
 			logger.debug("Reactions search complete!");
+			
+//			Map<String, String> reactionsIDS = null;
 
 			Map<String, String> reactionsIDS = Reports.generateKBaseReport(jobIdentification, organism, taxID, queryFileTotalOfGenes, properties, finalResults, service);
 
+			System.out.println("1");
+			
 			OutputMerlinFormat output = new OutputMerlinFormat(finalResults, modelMetabolites, reactionContainersByID);
 
+			System.out.println("2");
+			
 			Container container = new Container(output);
 			container.verifyDepBetweenClass();
 
-			String fileName = "sbml".concat("_qCov_").concat(Double.toString(properties.getQueryCoverage())).concat("_eValThresh_").concat(Double.toString(properties.geteValueThreshold())).concat(".json");
+			System.out.println("3");
+			
+			//			String fileName = "sbml".concat("_qCov_").concat(Double.toString(properties.getQueryCoverage())).concat("_eValThresh_").concat(Double.toString(properties.geteValueThreshold())).concat(".json");
 
-			TriageSBMLLevel3Writer sbml = new TriageSBMLLevel3Writer(path.concat("SBML\\").concat(fileName), container, taxID.toString(), false);
+			//			TriageSBMLLevel3Writer sbml = new TriageSBMLLevel3Writer(path.concat("SBML\\").concat(fileName), container, taxID.toString(), false);
 
-			sbml.writeToFile();
+			//			sbml.writeToFile();
 
 			validation(container, reactionsIDS, path); 
 
@@ -317,46 +368,142 @@ public class ProvideTransportReactionsToGenes {
 		}
 	}
 
-	/**
-	 * Merge the results of both methods
-	 * 
-	 * @param similaritiesResults