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Commit ad515ae2 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

small bugs fix, reference database inherit ids created

parent e9336c6f
...@@ -342,7 +342,7 @@ public class BlastAlignmentTransyt extends Observable implements ModelAlignments ...@@ -342,7 +342,7 @@ public class BlastAlignmentTransyt extends Observable implements ModelAlignments
} }
else{ else{
logger.info(iteration.getIteration().getIterationMessage().concat(" for {}"), queryID); logger.debug(iteration.getIteration().getIterationMessage().concat(" for {}"), queryID);
} }
} }
else{ else{
......
...@@ -8,7 +8,6 @@ import java.util.Set; ...@@ -8,7 +8,6 @@ import java.util.Set;
import org.neo4j.graphdb.GraphDatabaseService; import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.Node; import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.Relationship; import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.RelationshipType;
import org.neo4j.graphdb.Transaction; import org.neo4j.graphdb.Transaction;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
...@@ -23,7 +22,6 @@ import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.MetaboliteReferenc ...@@ -23,7 +22,6 @@ import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.MetaboliteReferenc
import pt.uminho.ceb.biosystems.transyt.utilities.files.JSONFilesUtils; import pt.uminho.ceb.biosystems.transyt.utilities.files.JSONFilesUtils;
import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties; import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties;
import pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.MetaboliteMajorLabel; import pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.MetaboliteMajorLabel;
import pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.MetabolitePropertyLabel;
import pt.uminho.sysbio.biosynth.integration.neo4j.BiodbMetaboliteNode; import pt.uminho.sysbio.biosynth.integration.neo4j.BiodbMetaboliteNode;
import pt.uminho.sysbio.biosynthframework.BiodbGraphDatabaseService; import pt.uminho.sysbio.biosynthframework.BiodbGraphDatabaseService;
...@@ -50,11 +48,11 @@ public class WriteByMetabolitesID { ...@@ -50,11 +48,11 @@ public class WriteByMetabolitesID {
Map<String, BiosynthMetaboliteProperties> data = getBiosynthDBData(service); Map<String, BiosynthMetaboliteProperties> data = getBiosynthDBData(service);
// Map<String, BiosynthMetaboliteProperties> data = null; // Map<String, BiosynthMetaboliteProperties> data = null;
// @SuppressWarnings("resource") @SuppressWarnings("resource")
// Scanner reader = new Scanner(System.in); Scanner reader = new Scanner(System.in);
// System.out.println("Writing Excel..."); // System.out.println("Writing Excel...");
// WriteExcel.writeNeo4jKeggInfo(data); // WriteExcel.writeNeo4jKeggInfo(data);
logger.info("Retrieving data from Biosynth database by metabolite name..."); logger.info("Retrieving data from Biosynth database by metabolite name...");
// //
...@@ -75,7 +73,6 @@ public class WriteByMetabolitesID { ...@@ -75,7 +73,6 @@ public class WriteByMetabolitesID {
// //
// Map<String, String[]> forChildsSearch = metabolitesIdentification.getforChildsSearch(); // Map<String, String[]> forChildsSearch = metabolitesIdentification.getforChildsSearch();
Map<String, Set<TcNumberContainer2>> newData = test(namesAndIDsContainer, data, service, reactionsData, properties); //uncomment
// int n = 1; // int n = 1;
// //
...@@ -83,10 +80,12 @@ public class WriteByMetabolitesID { ...@@ -83,10 +80,12 @@ public class WriteByMetabolitesID {
// //
// n = 99; // n = 99;
Map<String, Set<TcNumberContainer2>> newData = test(namesAndIDsContainer, data, service, reactionsData, properties); //uncomment
// test2(service, data, namesAndIDsContainer); // test2(service, data, namesAndIDsContainer);
new PopulateTransytNeo4jDatabase(data, newData, properties); //uncomment new PopulateTransytNeo4jDatabase(data, newData, properties); //uncomment
//
// System.out.println("Enter a random number to repeat (100 to repeat data retrieval) or 99 to finish: "); // System.out.println("Enter a random number to repeat (100 to repeat data retrieval) or 99 to finish: ");
// //
// try { // try {
...@@ -96,7 +95,7 @@ public class WriteByMetabolitesID { ...@@ -96,7 +95,7 @@ public class WriteByMetabolitesID {
// //
// n = reader.nextInt(); // n = reader.nextInt();
// } // }
//
// } // }
dataTx.failure(); dataTx.failure();
dataTx.close(); dataTx.close();
...@@ -233,7 +232,7 @@ public class WriteByMetabolitesID { ...@@ -233,7 +232,7 @@ public class WriteByMetabolitesID {
try { try {
// Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>(); // Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>();
// String[] accessions = new String[] {"Q2RIS7"}; // String[] accessions = new String[] {"P02931"};
// //
// for(String acc : accessions) // for(String acc : accessions)
// reactionsData2.put(acc, reactionsData.get(acc)); // reactionsData2.put(acc, reactionsData.get(acc));
...@@ -242,7 +241,7 @@ public class WriteByMetabolitesID { ...@@ -242,7 +241,7 @@ public class WriteByMetabolitesID {
Map<String, Set<TcNumberContainer2>> newData = new TransportReactionsBuilder(reactionsData, service, data, namesAndIDsContainer, properties).getResults(); //uncomment Map<String, Set<TcNumberContainer2>> newData = new TransportReactionsBuilder(reactionsData, service, data, namesAndIDsContainer, properties).getResults(); //uncomment
// for(TcNumberContainer2 container : newData.get("Q2RIS7")) { // for(TcNumberContainer2 container : newData.get("P02931")) {
// //
// System.out.println(container.getTcNumber()); // System.out.println(container.getTcNumber());
// //
......
...@@ -126,7 +126,7 @@ public class ProvideTransportReactionsToGenes { ...@@ -126,7 +126,7 @@ public class ProvideTransportReactionsToGenes {
Blast blast = new Blast(forceBlast, workFolderID, queryPath, properties); Blast blast = new Blast(forceBlast, workFolderID, queryPath, properties);
blastResults = blast.getAlignmentsByQuery(); blastResults = blast.getAlignmentsByQuery();
service = TransytNeo4jInitializer.getDatabaseService(true, properties); service = TransytNeo4jInitializer.getDatabaseService(properties);
// service = new TransytGraphDatabaseService(graphDatabaseService); // service = new TransytGraphDatabaseService(graphDatabaseService);
...@@ -493,12 +493,12 @@ public class ProvideTransportReactionsToGenes { ...@@ -493,12 +493,12 @@ public class ProvideTransportReactionsToGenes {
String tcNumber = capsule.getTcdbID(); String tcNumber = capsule.getTcdbID();
// if(tcNumber.equals("1.I.1.1.3")) { // if(tcNumber.equals("1.B.1.1.1")) {
// System.out.println(key); // System.out.println(key);
// System.out.println(tcNumber); // System.out.println(tcNumber);
// System.out.println(capsule.getEvalue() <= properties.geteValueThreshold()); // System.out.println(capsule.getEvalue() <= properties.geteValueThreshold());
// //
// } // }
if(!evaluesEntry.containsKey(tcNumber)) if(!evaluesEntry.containsKey(tcNumber))
evaluesEntry.put(tcNumber, capsule.getEvalue()); evaluesEntry.put(tcNumber, capsule.getEvalue());
...@@ -1155,7 +1155,8 @@ public class ProvideTransportReactionsToGenes { ...@@ -1155,7 +1155,8 @@ public class ProvideTransportReactionsToGenes {
for(String tcNumber : identifyTcNumbersForSearch) { for(String tcNumber : identifyTcNumbersForSearch) {
// System.out.println(tcNumber); // if(tcNumber.equalsIgnoreCase("1.B.1.1.1"))
// System.out.println(tcNumber);
try { try {
...@@ -1193,30 +1194,8 @@ public class ProvideTransportReactionsToGenes { ...@@ -1193,30 +1194,8 @@ public class ProvideTransportReactionsToGenes {
String reactionID = node.getProperty(TransytGeneralProperties.ReactionID); String reactionID = node.getProperty(TransytGeneralProperties.ReactionID);
// System.out.println(reactionID);
reversibility.put(reactionID, rev); reversibility.put(reactionID, rev);
// if(rel.hasProperty(TransytGeneralProperties.CompartimentalizedReactionID)) {
// String compReactionID = rel.getProperty(TransytGeneralProperties.CompartimentalizedReactionID);
//
// if(!rev)
// compReactionID = ReactionContainer.i.concat(compReactionID);
//
//// reactionID = reactionID.replaceAll("^i+", "i"); //ignore this line when problem in database is solved
//
// irreversibleIDs.put(reactionID, compReactionID);
// reactionID = compReactionID;
// }
// else if(!rev) {
// reactionID = ReactionContainer.i.concat(reactionID);
//// reactionID = reactionID.replaceAll("^i+", "i"); //ignore this line when problem in database is solved
// }
// System.out.println(reactionID);
ids.add(reactionID); ids.add(reactionID);
reactionNodes.add(node); reactionNodes.add(node);
} }
......
...@@ -88,7 +88,11 @@ public class ReactionsPredictor { ...@@ -88,7 +88,11 @@ public class ReactionsPredictor {
String tcNumber = capsule.getTcdbID(); String tcNumber = capsule.getTcdbID();
double simScore = capsule.getScore();
if(reactionsByTcNumber.containsKey(tcNumber)) { if(reactionsByTcNumber.containsKey(tcNumber)) {
// System.out.println(reactionsByTcNumber.get(tcNumber).contains("TR0000971"));
for(String reactionID : reactionsByTcNumber.get(tcNumber)) { for(String reactionID : reactionsByTcNumber.get(tcNumber)) {
...@@ -101,17 +105,20 @@ public class ReactionsPredictor { ...@@ -101,17 +105,20 @@ public class ReactionsPredictor {
hits.put(reactionID, hits.get(reactionID) + 1); hits.put(reactionID, hits.get(reactionID) + 1);
commonTaxaSum.put(reactionID, commonTaxaSum.get(reactionID) + taxaCount); commonTaxaSum.put(reactionID, commonTaxaSum.get(reactionID) + taxaCount);
reactionsSimilarity.put(reactionID, reactionsSimilarity.get(reactionID) + capsule.getBitScore()); reactionsSimilarity.put(reactionID, reactionsSimilarity.get(reactionID) + simScore);
} }
else { else {
hits.put(reactionID, 1); hits.put(reactionID, 1);
commonTaxaSum.put(reactionID, taxaCount); commonTaxaSum.put(reactionID, taxaCount);
reactionsSimilarity.put(reactionID, capsule.getBitScore()); reactionsSimilarity.put(reactionID, simScore);
} }
} }
// System.out.println(similaritySum + " + " + simScore);
similaritySum = similaritySum + simScore;//geneContainer.getSimilarities().get(capsule.getTarget());
similaritySum = similaritySum + capsule.getBitScore();//geneContainer.getSimilarities().get(capsule.getTarget()); // System.out.println(similaritySum);
} }
} }
...@@ -120,6 +127,9 @@ public class ReactionsPredictor { ...@@ -120,6 +127,9 @@ public class ReactionsPredictor {
Map<String, String> res = new HashMap<>(); Map<String, String> res = new HashMap<>();
for(String reactionID : allReactions) { for(String reactionID : allReactions) {
// if(reactionID.equals("TR0000971"))
// System.out.println(reactionID);
double gap = 0.0; double gap = 0.0;
...@@ -132,24 +142,21 @@ public class ReactionsPredictor { ...@@ -132,24 +142,21 @@ public class ReactionsPredictor {
// System.out.println("freqScore = " + reactionsSimilarity.get(reactionID) + " / " + similaritySum); // System.out.println("freqScore = " + reactionsSimilarity.get(reactionID) + " / " + similaritySum);
// System.out.println("taxScore = " + commonTaxaSum.get(reactionID) + " * " + (1-gap * BETA)+ " / " + hit * tMax); // System.out.println("taxScore = " + commonTaxaSum.get(reactionID) + " * " + (1-gap * properties.getBeta())+ " / " + hit * tMax);
double freqScore = reactionsSimilarity.get(reactionID) / similaritySum; double freqScore = reactionsSimilarity.get(reactionID) / similaritySum;
double taxScore = commonTaxaSum.get(reactionID) * (1-gap * properties.getBeta()) / (hit * tMax); double taxScore = commonTaxaSum.get(reactionID) * (1-gap * properties.getBeta()) / (hit * tMax);
Double score = properties.getAlpha() * freqScore + (1-properties.getAlpha()) * taxScore; Double score = properties.getAlpha() * freqScore + (1-properties.getAlpha()) * taxScore;
// System.out.println(reactionID + " ---->>> \t" + ALPHA + " * " + freqScore + " + (1 - " + ALPHA + " ) * " + taxScore + " = " + score) ; // System.out.println(reactionID + " ---->>> \t" + properties.getAlpha() + " * " + freqScore + " + (1 - " + properties.getAlpha() + " ) * " + taxScore + " = " + score) ;
if(score > properties.getReactionsAnnotationScoreThreshold()) { if(score > properties.getReactionsAnnotationScoreThreshold()) {
// System.out.println(reactionID + "\t" + score); // System.out.println(reactionID + "\t" + score);
//
// System.out.println(score == Double.MAX_VALUE);
res.put(reactionID, Double.toString(score)); res.put(reactionID, Double.toString(score));
} }
} }
} }
......
...@@ -17,14 +17,14 @@ import org.slf4j.LoggerFactory; ...@@ -17,14 +17,14 @@ import org.slf4j.LoggerFactory;
import pt.uminho.ceb.biosystems.transyt.service.containers.BiosynthMetabolites; import pt.uminho.ceb.biosystems.transyt.service.containers.BiosynthMetabolites;
import pt.uminho.ceb.biosystems.transyt.service.relations.MetabolitesChilds; import pt.uminho.ceb.biosystems.transyt.service.relations.MetabolitesChilds;
import pt.uminho.ceb.biosystems.transyt.service.utilities.FileUtils; import pt.uminho.ceb.biosystems.transyt.service.transytDatabase.TransytNeo4jInitializer;
import pt.uminho.ceb.biosystems.transyt.service.utilities.MappingMetabolites; import pt.uminho.ceb.biosystems.transyt.service.utilities.MappingMetabolites;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.BiosynthMetaboliteProperties; import pt.uminho.ceb.biosystems.transyt.utilities.capsules.BiosynthMetaboliteProperties;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.ReactionContainer; import pt.uminho.ceb.biosystems.transyt.utilities.capsules.ReactionContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.TcNumberContainer2; import pt.uminho.ceb.biosystems.transyt.utilities.capsules.TcNumberContainer2;
import pt.uminho.ceb.biosystems.transyt.utilities.dictionary.Synonyms; import pt.uminho.ceb.biosystems.transyt.utilities.dictionary.Synonyms;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.MetaboliteReferenceDatabaseEnum;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.TypeOfTransporter; import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.TypeOfTransporter;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.MetaboliteReferenceDatabaseEnum;
import pt.uminho.ceb.biosystems.transyt.utilities.files.FilesUtils; import pt.uminho.ceb.biosystems.transyt.utilities.files.FilesUtils;
import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties; import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties;
import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Utilities; import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Utilities;
...@@ -33,16 +33,11 @@ import pt.uminho.sysbio.biosynthframework.BiodbGraphDatabaseService; ...@@ -33,16 +33,11 @@ import pt.uminho.sysbio.biosynthframework.BiodbGraphDatabaseService;
public class TransportReactionsBuilder { public class TransportReactionsBuilder {
// private String reactionsIDsPath = "reactionsIDS.txt";
// private String reactionsIDSTranslationPath = "reactionsIDSTranslation.txt";
// private Map<String, String> reactionsIDsMap;
// private Map<String, String> reactionsIDsMapTranslation;
private Map<String, Set<TcNumberContainer2>> newData; private Map<String, Set<TcNumberContainer2>> newData;
private Map<String, BiosynthMetaboliteProperties> allData; private Map<String, BiosynthMetaboliteProperties> allData;
private Map<String, String> element_map = FormulaParser.getSymbolMap(); private Map<String, String> element_map = FormulaParser.getSymbolMap();
private Map<String, String> allExistingReactions = FilesUtils.readMapFromFile(FilesUtils.getReactionsIdentifiersFilePath()); private Map<String, String> allExistingReactions; // = FilesUtils.readMapFromFile(FilesUtils.getReactionsIdentifiersFilePath());
private Map<String, String> newReactionIDs; // private Map<String, String> newReactionIDs;
private Map<String, Integer> generationsLimit; private Map<String, Integer> generationsLimit;
private Map<String, String> mappingModelSeed; private Map<String, String> mappingModelSeed;
private Map<String, String> mappingBiGG; private Map<String, String> mappingBiGG;
...@@ -69,12 +64,11 @@ public class TransportReactionsBuilder { ...@@ -69,12 +64,11 @@ public class TransportReactionsBuilder {
public TransportReactionsBuilder(Map<String, Set<TcNumberContainer2>> reactionsData, BiodbGraphDatabaseService service, public TransportReactionsBuilder(Map<String, Set<TcNumberContainer2>> reactionsData, BiodbGraphDatabaseService service,
Map<String, BiosynthMetaboliteProperties> allData, BiosynthMetabolites biosynthMetabolites, Properties properties) { Map<String, BiosynthMetaboliteProperties> allData, BiosynthMetabolites biosynthMetabolites, Properties properties) {
this.allExistingReactions = TransytNeo4jInitializer.getAllReactionsIdentifiersInReferenceDatabase(properties);
// String path = FilesUtils.getReactionsBuilderFilesDirectory();
this.allData = allData; this.allData = allData;
this.newData = new HashMap<>(); this.newData = new HashMap<>();
this.newReactionIDs = new HashMap<>(); // this.newReactionIDs = new HashMap<>();
// this.tcdbMetabolitesIDs = tcdbMetabolitesIDs; // this.tcdbMetabolitesIDs = tcdbMetabolitesIDs;
this.allMetabolitesIDs = biosynthMetabolites.getMetabolitesIDs(); this.allMetabolitesIDs = biosynthMetabolites.getMetabolitesIDs();
...@@ -378,7 +372,7 @@ public class TransportReactionsBuilder { ...@@ -378,7 +372,7 @@ public class TransportReactionsBuilder {
newData.put(accession, setTcContainers); newData.put(accession, setTcContainers);
} }
FilesUtils.addMapToFile(FilesUtils.getReactionsIdentifiersFilePath(), this.newReactionIDs); // FilesUtils.addMapToFile(FilesUtils.getReactionsIdentifiersFilePath(), this.newReactionIDs);
// logger.info(" All TranSyT reactions generated!!!"); //CHECK THESE COUNTERS // logger.info(" All TranSyT reactions generated!!!"); //CHECK THESE COUNTERS
// logger.debug("TOTAl of reactions generated (not filtered): {}", reactionsCounter); // logger.debug("TOTAl of reactions generated (not filtered): {}", reactionsCounter);
...@@ -725,7 +719,7 @@ public class TransportReactionsBuilder { ...@@ -725,7 +719,7 @@ public class TransportReactionsBuilder {
} }
else { else {
this.allExistingReactions.put(metaId, newReactContainer.getReactionID()); this.allExistingReactions.put(metaId, newReactContainer.getReactionID());
this.newReactionIDs.put(metaId, newReactContainer.getReactionID()); // this.newReactionIDs.put(metaId, newReactContainer.getReactionID());
} }
reactionsGenerated.put(newReactContainer, isChild); reactionsGenerated.put(newReactContainer, isChild);
......
package pt.uminho.ceb.biosystems.transyt.service.transyt; package pt.uminho.ceb.biosystems.transyt.service.transyt;
import java.util.Map;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import pt.uminho.ceb.biosystems.transyt.scraper.tcdb.tcdbTransportTypesRetriever.Retriever; import pt.uminho.ceb.biosystems.transyt.scraper.tcdb.tcdbTransportTypesRetriever.Retriever;
import pt.uminho.ceb.biosystems.transyt.service.internalDB.WriteByMetabolitesID; import pt.uminho.ceb.biosystems.transyt.service.internalDB.WriteByMetabolitesID;
import pt.uminho.ceb.biosystems.transyt.service.reactions.ProvideTransportReactionsToGenes; import pt.uminho.ceb.biosystems.transyt.service.reactions.ProvideTransportReactionsToGenes;
import pt.uminho.ceb.biosystems.transyt.service.transytDatabase.TransytNeo4jInitializer;
import pt.uminho.ceb.biosystems.transyt.service.utilities.OrganismProperties; import pt.uminho.ceb.biosystems.transyt.service.utilities.OrganismProperties;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.Organism; import pt.uminho.ceb.biosystems.transyt.utilities.capsules.Organism;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.STAIN; import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.STAIN;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.MetaboliteReferenceDatabaseEnum;
import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties; import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties;
/** /**
...@@ -28,17 +30,17 @@ public class TransyTestMain { ...@@ -28,17 +30,17 @@ public class TransyTestMain {
// JSONFilesUtils.readJSONtcdbReactionsFile(); // JSONFilesUtils.readJSONtcdbReactionsFile();
// System.exit(0);
// //
Properties properties = new Properties(); Properties properties = new Properties();
String path = "/Users/davidelagoa/Desktop/ecoli/ecoli_iAF1260b/"; String path = "/Users/davidelagoa/Desktop/ecoli/ecoli_iML1515/";
String filePath = path + "protein.faa"; String filePath = path + "protein.faa";
String modelPath = path + "model.xml"; String modelPath = path + "model.xml";
String command = "1"; String command = "3";
String resultPath = path + "results_e#1/"; String resultPath = path + "results_e#1/";
...@@ -95,7 +97,11 @@ public class TransyTestMain { ...@@ -95,7 +97,11 @@ public class TransyTestMain {
// resultPath = workFolderID.concat("transyt.xml"); // resultPath = workFolderID.concat("transyt.xml");
// } // }
properties.setDefaultLabel(MetaboliteReferenceDatabaseEnum.BiGG); // properties.setDefaultLabel(MetaboliteReferenceDatabaseEnum.BiGG);
properties.setTaxID(511145);
properties.setOverrideCommonOntologyFilter(true);
properties.setDatabaseURI("bolt://localhost:7687");
Organism organism = new OrganismProperties(properties, stain).getOrganism(); Organism organism = new OrganismProperties(properties, stain).getOrganism();
...@@ -103,7 +109,7 @@ public class TransyTestMain { ...@@ -103,7 +109,7 @@ public class TransyTestMain {
// String modelPath = args[2]; // String modelPath = args[2];
new ProvideTransportReactionsToGenes(workFolderID, organism, filePath, modelPath, new ProvideTransportReactionsToGenes(workFolderID, organism, filePath, modelPath,
metabolitesPath, resultPath, properties, false); //29421 - Nitrobacter vulgaris metabolitesPath, resultPath, properties, false);
break; break;
......
package pt.uminho.ceb.biosystems.transyt.service.transyt; package pt.uminho.ceb.biosystems.transyt.service.transyt;
import java.io.IOException;
import java.util.List;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
...@@ -12,8 +9,6 @@ import pt.uminho.ceb.biosystems.transyt.service.reactions.ProvideTransportReacti ...@@ -12,8 +9,6 @@ import pt.uminho.ceb.biosystems.transyt.service.reactions.ProvideTransportReacti
import pt.uminho.ceb.biosystems.transyt.service.utilities.OrganismProperties; import pt.uminho.ceb.biosystems.transyt.service.utilities.OrganismProperties;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.Organism; import pt.uminho.ceb.biosystems.transyt.utilities.capsules.Organism;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.STAIN; import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.STAIN;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.MetaboliteReferenceDatabaseEnum;
import pt.uminho.ceb.biosystems.transyt.utilities.files.FilesUtils;
import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties; import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties;
/** /**
...@@ -28,7 +23,7 @@ public class TransytMain { ...@@ -28,7 +23,7 @@ public class TransytMain {
// Integer taxID = Integer.valueOf(args[0]); // Integer taxID = Integer.valueOf(args[0]);
logger.info("############################################ TranSyT - v0.0.10-SNAPSHOT ############################################"); logger.info("############################################ TranSyT - v0.0.10.2-SNAPSHOT ############################################");
String command = args[0]; String command = args[0];
......