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Commit 307fa04a authored by Davide Lagoa's avatar Davide Lagoa
Browse files

reactions generator system modified

parent bb751175
......@@ -10,6 +10,11 @@
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.hibernate.eclipse.console.hibernateBuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
......@@ -19,5 +24,6 @@
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>org.hibernate.eclipse.console.hibernateNature</nature>
</natures>
</projectDescription>
......@@ -8,7 +8,9 @@ org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.release=enabled
org.eclipse.jdt.core.compiler.source=10
default.configuration=transyt-scraper
eclipse.preferences.version=1
hibernate3.enabled=true
......@@ -5,7 +5,7 @@
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>scraper</artifactId>
<version>0.0.1-SNAPSHOT</version>
<version>0.0.5-SNAPSHOT</version>
<packaging>jar</packaging>
<name>scraper</name>
......@@ -66,7 +66,7 @@
<dependency>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>utilities</artifactId>
<version>0.0.1-SNAPSHOT</version>
<version>0.0.5-SNAPSHOT</version>
</dependency>
<dependency>
......
......@@ -8,7 +8,6 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.poi.ss.formula.functions.T;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
......@@ -16,7 +15,7 @@ import pt.uminho.ceb.biosystems.transyt.utilities.capsules.ReactionContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.TcNumberContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.TcdbMetabolitesContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.dictionary.Synonyms;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.TypeOfTransporter;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.TypeOfTransporter;
import pt.uminho.ceb.biosystems.transyt.utilities.files.FilesUtils;
public class GenerateTransportReactions {
......@@ -44,7 +43,7 @@ public class GenerateTransportReactions {
// Map<String, TcdbMetabolitesContainer> tcdbMetabolites2 = new HashMap<>();
//
// tcdbMetabolites2.put("O32167", tcdbMetabolites.get("O32167"));
// tcdbMetabolites2.put("B5BRC2", tcdbMetabolites.get("B5BRC2"));
for(String accession : tcdbMetabolites.keySet()) {
......@@ -133,7 +132,6 @@ public class GenerateTransportReactions {
if(evidence == null) {
if(reactionContainer.getTransportType().equals(TypeOfTransporter.PEPdependent))
newTcContainer = processPEPReactions(tcNumber+" "+accession, reactionContainer.getReaction(), "PEP-0" , reactionContainer.getProperties(), metabolites, newTcContainer);
......
......@@ -16,7 +16,7 @@ import org.jsoup.nodes.Document;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.ReactionContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.TcNumberContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.connection.LinkConnection;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.TypeOfTransporter;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.TypeOfTransporter;
/**
* @author Davide
......@@ -505,5 +505,4 @@ public class FindTransportTypes {
return null;
}
}
......@@ -24,7 +24,7 @@ import pt.uminho.ceb.biosystems.transyt.utilities.capsules.TcNumberContainer;
import pt.uminho.ceb.biosystems.transyt.utilities.connection.LinkConnection;
import pt.uminho.ceb.biosystems.transyt.utilities.connection.TcdbExplorer;
import pt.uminho.ceb.biosystems.transyt.utilities.connection.TcdbRetriever;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.TypeOfTransporter;
import pt.uminho.ceb.biosystems.transyt.utilities.enumerators.Enumerators.TypeOfTransporter;
import pt.uminho.ceb.biosystems.transyt.utilities.files.FilesUtils;
import pt.uminho.ceb.biosystems.transyt.utilities.files.JSONFilesUtils;
......@@ -163,7 +163,7 @@ public class FindTransporters {
if(failed.size() > 0)
logger.warn("The following queries failed: {}", failed.toString());
JSONFilesUtils.writeJSONtcFamilyReactions(data);
}
......@@ -593,9 +593,13 @@ public class FindTransporters {
if((reactantsMetab.size() == 1 && productsMetab.size() == 1))
return TypeOfTransporter.Uniport;
else if((reactantsMetab.size() > reactantsComp.size()) && reactantsComp.size() == 1)
else if((reactantsMetab.size() > reactantsComp.size()) && reactantsComp.size() == 1) {
if(reactantsMetab.size() == 2 && reaction.getReactant().matches(".*\\s+[^\\+]*.*\\(\\s*and.*")) //false positive. Ex: "Ca2+ (and other cations) (out)"
return TypeOfTransporter.Uniport;
return TypeOfTransporter.Symport;
}
// else if(reactantsComp.size() == 1 && reactantsMetab.size() == 1)
// return TypeOfTransporter.Uniport;
......
......@@ -34,14 +34,14 @@ public class Retriever {
logger.info("Retrieving TCDB FASTA file...");
TcdbRetriever.getSubstrates();
// TcdbRetriever.getSubstrates();
Set<String> tcNumbers = TcdbExplorer.getTcNumbers(true);
Set<String> toSearch = TcdbExplorer.generateTCsFamily(tcNumbers);
FindTransporters.saveAllTCFamiliesInformation(toSearch);
//
Map<String, String> proteinFamilyDescription = TcdbExplorer.getProteinsBelongingToFamilyDescription(tcNumbers);
FilesUtils.saveMapInFile(FilesUtils.getBackupFamilyDescriptionsFilesDirectory().concat("familyDescription.txt"), proteinFamilyDescription);
......
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