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Commit 17f64607 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

minor improvements, modelseedAPI added, conjugated pairs exception created

parent 290a4d49
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Showing with 1112 additions and 550 deletions
src/main/java/pt/uminho/ceb/biosystems/transyt/service/blast/Blast.java
View file @ 17f64607
......@@ -49,14 +49,11 @@ public class Blast implements Observer{
private Integer queryFileSize = 0;
private Properties properties;
private String queryFilePath;
private boolean forceBlast;
public Blast(boolean forceBlast, String workFolderID, String queryFilePath, Properties properties) {
public Blast(String workFolderID, String queryFilePath, Properties properties) {
try {
this.forceBlast = forceBlast;
logger.info("Blast process initializing...");
this.properties = properties;
......@@ -100,7 +97,7 @@ public class Blast implements Observer{
logger.info("Blast process initialized!");
RunSimilaritySearchTransyt run_similaritySearch = new RunSimilaritySearchTransyt(forceBlast, properties.getSimilarityThreshold(),
RunSimilaritySearchTransyt run_similaritySearch = new RunSimilaritySearchTransyt(properties.isForceBlast(), properties.getSimilarityThreshold(),
Method.SmithWaterman, sequences, new AtomicBoolean(false), new AtomicInteger(0), AlignmentScoreType.ALIGNMENT);
run_similaritySearch.setSubjectFastaFilePath(tcdbFastaFile);
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/blast/BlastAlignmentTransyt.java
View file @ 17f64607
......@@ -125,9 +125,7 @@ public class BlastAlignmentTransyt extends Observable implements ModelAlignments
outputFile.getParentFile().mkdirs();
// System.out.println(outputFile.getAbsolutePath());
// System.out.println(outputFile.getAbsolutePath());
if(forceBlast) {
......@@ -197,7 +195,10 @@ public class BlastAlignmentTransyt extends Observable implements ModelAlignments
String queryID = iteration.getQueryDef().trim();
Integer queryLength = iteration.getQueryLen();
// if(queryID.equals("b2169"))
// System.out.println();
String [] query_array;
String query_org = "";
String queryLocus = "";
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/blast/RunSimilaritySearchTransyt.java
View file @ 17f64607
......@@ -101,7 +101,7 @@ public class RunSimilaritySearchTransyt extends Observable implements Observer {
// ConcurrentLinkedQueue<String> queryArray = new ConcurrentLinkedQueue<String>(this.querySequences.keySet());
int numberOfCores = Runtime.getRuntime().availableProcessors();
//int numberOfCores = new Double(Runtime.getRuntime().availableProcessors()*1.5).intValue();
if(this.querySequences.keySet().size()<numberOfCores)
numberOfCores=this.querySequences.keySet().size();
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/internalDB/FetchCompoundsByName.java
View file @ 17f64607
......@@ -77,8 +77,8 @@ public class FetchCompoundsByName {
getNamesMethod1();
getNamesMethod2();
forReplacement.put("cpd02416", "cpd00122");
// forReplacement.put("cpd20862", "cpd00082");
forReplacement.put("cpd02416", "cpd00122");
forReplacement.put("cpd11665", "cpd15291");
for(String s : compounds.keySet()) {
......@@ -236,7 +236,7 @@ public class FetchCompoundsByName {
Set<String> names = getSynonyms(node, nodeProperties, service);
if(entryID.matches("META:.*"))
if(entryID.matches("META:.*") || entryID.matches("cpd.*"))
names.add(entryID);
for(String name : names) {
......@@ -401,11 +401,11 @@ public class FetchCompoundsByName {
// }
}
if(name.equalsIgnoreCase("Solute"))
System.out.println();
if(Utilities.processBiosynthName(name).equalsIgnoreCase("Solute"))
System.out.println();
// if(name.equalsIgnoreCase("Solute"))
// System.out.println();
//
// if(Utilities.processBiosynthName(name).equalsIgnoreCase("Solute"))
// System.out.println();
compounds.put(Utilities.processBiosynthName(name), references);
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/internalDB/WriteByMetabolitesID.java
View file @ 17f64607
package pt.uminho.ceb.biosystems.transyt.service.internalDB;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Scanner;
import java.util.Set;
import java.util.stream.Collectors;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.RelationshipType;
import org.neo4j.graphdb.Transaction;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
......@@ -16,7 +17,6 @@ import org.slf4j.LoggerFactory;
import pt.uminho.ceb.biosystems.transyt.scraper.tcdb.tcdbTransportTypesRetriever.Retriever;
import pt.uminho.ceb.biosystems.transyt.service.biosynth.initializeNeo4jdb;
import pt.uminho.ceb.biosystems.transyt.service.containers.BiosynthMetabolites;
import pt.uminho.ceb.biosystems.transyt.service.reactions.IdentifyReactionsMetabolites;
import pt.uminho.ceb.biosystems.transyt.service.reactions.TransportReactionsBuilder;
import pt.uminho.ceb.biosystems.transyt.service.transytDatabase.PopulateTransytNeo4jDatabase;
import pt.uminho.ceb.biosystems.transyt.utilities.capsules.BiosynthMetaboliteProperties;
......@@ -86,12 +86,12 @@ public class WriteByMetabolitesID {
} catch (Exception e) {
e.printStackTrace();
n = reader.nextInt();
n = 1;
}
}
}
else {
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, false).getResults(); //uncomment
new PopulateTransytNeo4jDatabase(data, newData, properties);
}
......@@ -127,17 +127,21 @@ public class WriteByMetabolitesID {
// }
// }
Node node = service.getNodeByEntryAndLabel("META:CPD0-2232", MetaboliteMajorLabel.MetaCyc);
Node node = service.getNodeByEntryAndLabel("META:Ions", MetaboliteMajorLabel.MetaCyc);
System.out.println(node.getAllProperties());
// Iterable<Relationship> rels = node.getRelationships();
//
// for(Relationship rel : rels) {
// Long otherNode = rel.getOtherNodeId(node.getId());
// Node node = service.getNodeByEntryAndLabel("cpd15460", MetaboliteMajorLabel.ModelSeed);
//
// System.out.println(service.getNodeById(otherNode).getAllProperties());
// }
// System.out.println(node.getAllProperties());
// Iterable<Relationship> rels = node.getRelationships();
//
// for(Relationship rel : rels) {
// Long otherNode = rel.getOtherNodeId(node.getId());
//
// System.out.println(service.getNodeById(otherNode).getAllProperties());
// }
......@@ -151,55 +155,65 @@ public class WriteByMetabolitesID {
@SuppressWarnings("unused")
public static Map<String, Set<TcNumberContainer2>> test(BiosynthMetabolites namesAndIDsContainer, Map<String, BiosynthMetaboliteProperties> data, BiodbGraphDatabaseService service,
Map<String, Set<TcNumberContainer2>> reactionsData, Properties properties) {
try {
Boolean generate = true;
String accession = "P04840";
String accession = "Q8DL32"; //
// test2(service, null, null);
Retriever.runRetriever(true, true, accession);
if(generate) {
reactionsData = JSONFilesUtils.readJSONtcdbReactionsFile();
Map<String, Set<TcNumberContainer2>> reactionsData2 = new HashMap<>();
String[] accessions = new String[] {accession};
for(String acc : accessions)
reactionsData2.put(acc, reactionsData.get(acc));
if(accession == null) {
reactionsData2 = new HashMap<>(reactionsData);
}
else {
String[] accessions = new String[] {accession};
for(String acc : accessions)
reactionsData2.put(acc, reactionsData.get(acc));
}
/////TRANSYT
Map<String, Set<TcNumberContainer2>> newData = new TransportReactionsBuilder(reactionsData2, service, data, namesAndIDsContainer, properties).getResults(); //uncomment
for(TcNumberContainer2 container : newData.get(accession)) {
Map<String, Set<TcNumberContainer2>> newData = new TransportReactionsBuilder(reactionsData2, service, data, namesAndIDsContainer, properties, true).getResults(); //uncomment
if(accession != null) {
for(TcNumberContainer2 container : newData.get(accession)) {
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).getMetaReactionID());
System.out.println(container.getReactionContainer(id).getCompartmentalizedReactionID());
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(container.getReactionContainer(id).getOriginalReaction());
List<String> reactions = container.getReactionContainer(id).getModelseedReactionIdentifiers();
if(reactions != null)
System.out.println(reactions.stream().map(i -> i.toString()).collect(Collectors.joining(";")));
}
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).getMetaReactionID());
System.out.println(container.getReactionContainer(id).getCompartmentalizedReactionID());
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(container.getReactionContainer(id).getOriginalReaction());
}
System.out.println();
}
// new PopulateTransytNeo4jDatabase(data, newData, properties);
// new PopulateTransytNeo4jDatabase(data, newData, properties);
}
// JSONFilesUtils.writeJSONTriageReactions(newData);
......@@ -246,11 +260,8 @@ public class WriteByMetabolitesID {
BiosynthMetaboliteProperties bioSynMetab;
Set<String> synonyms = FetchCompoundsByName.getSynonyms(node, nodeProperties, service);
// if(entryID.matches("META:CPD-9781") || entryID.matches("META:CPD0-2232"))
// System.out.println();
if(entryID.matches("META:.*")) {
if(entryID.matches("META:.*") || entryID.matches("cpd.*")) {
synonyms.add(entryID);
}
// String names ="";
......@@ -276,10 +287,10 @@ public class WriteByMetabolitesID {
bioSynMetab = new BiosynthMetaboliteProperties(entryID, nodeProperties.get("major_label").toString(), synonyms);
else
bioSynMetab = new BiosynthMetaboliteProperties(entryID, BiosynthMetaboliteProperties.NONE, synonyms);
if(node.hasProperty("formula")) {
String formula = (String) nodeProperties.get("formula");
if(formula != null && !(formula.equalsIgnoreCase("none") || formula.equalsIgnoreCase("null")))
bioSynMetab.setFormula(formula);
}
......@@ -292,7 +303,9 @@ public class WriteByMetabolitesID {
bioSynMetab.setFormula("C4H6N2O3R2"); //there's an error in the database, it needs to be updated
else if(entryID.equalsIgnoreCase("cpd28237"))
bioSynMetab.setFormula("C6H8N3O4R3"); //there's an error in the database, it needs to be updated
else if(entryID.equalsIgnoreCase("cpd16486"))
bioSynMetab.setFormula("C13H18O2"); //there's an error in the database, it needs to be updated
if(node.hasProperty("remark"))
bioSynMetab.setRemark((String) nodeProperties.get("remark"));
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/kbase/ModelSEEDCompoundsFileReader.java → src/main/java/pt/uminho/ceb/biosystems/transyt/service/kbase/ModelSEEDRealatedOperations.java
View file @ 17f64607
package pt.uminho.ceb.biosystems.transyt.service.kbase;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
public class ModelSEEDCompoundsFileReader {
import pt.uminho.ceb.biosystems.transyt.scraper.APIs.ModelSEEDAPI;
import pt.uminho.ceb.biosystems.transyt.service.neo4jRest.RestNeo4jGraphDatabase;
import pt.uminho.ceb.biosystems.transyt.service.transytDatabase.TransytNeo4jInitializer;
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.files.FilesUtils;
import pt.uminho.ceb.biosystems.transyt.utilities.transytUtilities.Properties;
public class ModelSEEDRealatedOperations {
/**
* Method to read JSON exceptions file.
......@@ -101,4 +112,151 @@ public class ModelSEEDCompoundsFileReader {
return data;
}
public static void assingModelSEEDIdentifiersToTranSyTReactions(boolean useCache, Map<String, Set<TcNumberContainer2>> data) throws Exception {
Map<String, List<String>> reactionsMapping = new HashMap<>();
Map<String, String> modelseedReactions = ModelSEEDAPI.getModelseedReaction(useCache);
Map<String, String> notFound = new HashMap<>();
Map<String, List<String>> msReactants = new HashMap<>();
Map<String, List<String>> msProducts = new HashMap<>();
Map<String, Boolean> msReversible = new HashMap<>();
for(String identifier : modelseedReactions.keySet()) {
String reaction = modelseedReactions.get(identifier);
String[] splitReaction = reaction.split("<*=>*");
if(splitReaction.length > 1 && splitReaction[0].trim().length() > 0 && splitReaction[1].trim().length() > 0) {
msReactants.put(identifier, rearrangeModelSEEDReactant(splitReaction[0]));
msProducts.put(identifier, rearrangeModelSEEDReactant(splitReaction[1]));
// if(splitReaction[0].contains("cpd00066") && splitReaction[1].contains("cpd00066") &&
// splitReaction[0].contains("cpd00067") && splitReaction[1].contains("cpd00067"))
// System.out.println(identifier + "\t" + reaction);
if(reaction.contains("<=>"))
msReversible.put(identifier, true);
else
msReversible.put(identifier, false);
}
}
for(String accession : data.keySet()) {
for(TcNumberContainer2 tcContainer : data.get(accession)) {
for(Integer key : tcContainer.getAllReactionsIds()) {
ReactionContainer container = tcContainer.getReactionContainer(key);
String transytIdentifier = container.getReactionID();
if(reactionsMapping.containsKey(transytIdentifier)) {
if(reactionsMapping.get(transytIdentifier) != null) {
for(String modelseedIdentifier : reactionsMapping.get(transytIdentifier))
container.addModelseedReactionIdentifier(modelseedIdentifier);
}
}
else {
String[] splitReaction = container.getReactionModelSEED().split(container.getDirectionRegex());
List<String> transytReactant = rearrangeTransytReactant(splitReaction[0]);
List<String> transytProduct = rearrangeTransytReactant(splitReaction[1]);
for(String modelSeedIdentifier : msReversible.keySet()) {
// if(modelSeedIdentifier.equals("rxn27378")) {
// System.out.println(msReactants.get(modelSeedIdentifier));
// System.out.println(transytReactant);
// System.out.println(msProducts.get(modelSeedIdentifier));
// System.out.println(transytProduct);
// }
if(container.isReversible() == msReversible.get(modelSeedIdentifier)) {
boolean save = false;
if(transytReactant.containsAll(msReactants.get(modelSeedIdentifier)) &&
msReactants.get(modelSeedIdentifier).containsAll(transytReactant) &&
transytProduct.containsAll(msProducts.get(modelSeedIdentifier)) &&
msProducts.get(modelSeedIdentifier).containsAll(transytProduct)) {
save = true;
}
else if(container.isReversible() && transytReactant.containsAll(msProducts.get(modelSeedIdentifier)) &&
msReactants.get(modelSeedIdentifier).containsAll(transytProduct) &&
transytProduct.containsAll(msReactants.get(modelSeedIdentifier)) &&
msProducts.get(modelSeedIdentifier).containsAll(transytReactant)) {
save = true;
}
if(save) {
if(!reactionsMapping.containsKey(transytIdentifier))
reactionsMapping.put(transytIdentifier, new ArrayList<>());
reactionsMapping.get(transytIdentifier).add(modelSeedIdentifier);
container.addModelseedReactionIdentifier(modelSeedIdentifier);
}
}
}
if(container.getModelseedReactionIdentifiers() == null) {
reactionsMapping.put(transytIdentifier, null);
// System.out.println(transytIdentifier + "\t" + container.getReactionModelSEED());
notFound.put(transytIdentifier, container.getReactionModelSEED());
}
}
}
}
}
// FilesUtils.saveMapInFile("/Users/davidelagoa/Desktop/notFound.txt", notFound);
}
/**
* @param reactant
* @return
*/
private static List<String> rearrangeModelSEEDReactant(String reactant){
List<String> components = new ArrayList<>();
String[] reactantSplit = reactant.split("\\+");
for(String component : reactantSplit) {
component = component.replace("(", "").replaceAll("\\)\\s+", ""); //stoichiometry
component = component.replace("[0]", "(in)").replace("[1]", "(out)").replace("[2]", "(middle)"); //compartments
components.add(component.replaceAll("\\s+", "").replaceAll("^1cpd", "cpd").trim());
}
return components;
}
/**
* @param reactant
* @return
*/
private static List<String> rearrangeTransytReactant(String reactant){
List<String> components = new ArrayList<>();
String[] reactantSplit = reactant.split("\\+");
for(String component : reactantSplit) {
if(!component.contains("in") && !component.contains("out") && !component.contains("middle"))
component = component.concat("(in)");
components.add(component.replaceAll("\\s+", "").trim());
}
return components;
}
}
src/main/java/pt/uminho/ceb/biosystems/transyt/service/kbase/Reports.java
View file @ 17f64607
......@@ -255,6 +255,9 @@ public class Reports {
reportPath = reportPath.concat("scoresMethod1.txt");
System.out.println(reportByEvalue.containsKey("b3201"));
System.out.println(reportByEvalueAux.containsKey("b3201"));
try {
PrintWriter writer = new PrintWriter(reportPath, "UTF-8");
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/neo4jRest/RestNeo4jGraphDatabase.java
View file @ 17f64607
......@@ -711,6 +711,35 @@ public class RestNeo4jGraphDatabase implements AutoCloseable{
return map;
}
/**
* Retrieve the transport type of all reactions.
*
* @return
*/
public Map<String, TypeOfTransporter> getAllReactionHasTransportType() {
Map<String, TypeOfTransporter> map = new HashMap<>();
Session session = driver.session();
Result res = session.run(
"MATCH (a:" + TransytNodeLabel.Reaction + ")-[t:" + TransytRelationshipType.has_transport_type + "]->(b) "
+ "RETURN {reactid:a." + TransytGeneralProperties.ReactionID + ", type:b." + TransytGeneralProperties.Transport_Type + "}");
while(res.hasNext()) {
Record record = res.next();
String reactionID = record.get(0).asMap().get("reactid").toString();
String transportType = record.get(0).asMap().get("type").toString();
map.put(reactionID, TypeOfTransporter.valueOf(transportType));
}
session.close();
return map;
}
/**
* Find the moleculas formulas of each metabolite.
*
......@@ -912,6 +941,8 @@ public class RestNeo4jGraphDatabase implements AutoCloseable{
// System.out.println(rel.getEndNode().getAllProperties());
metaboliteID = node.getProperty(TransytGeneralProperties.MetaboliteID);
metaboliteID = metaboliteID.replace(" (middle)", "").trim(); //delete when fixed
if(metaboliteID == null)
return null;
......
src/main/java/pt/uminho/ceb/biosystems/transyt/service/reactions/IdentifyReactionsMetabolites.java
View file @ 17f64607
......@@ -31,17 +31,16 @@ public class IdentifyReactionsMetabolites {
private Map<String, Set<String>> metabolites;
private Map<String, String[]> forChildsSearch;
private Map<String, String> metabolitesByOriginalName = new HashMap<String, String>();
private Map<String, BiosynthMetaboliteProperties> allData;
private MetaboliteMajorLabel overrideDefauldLabel;
private Synonyms dictionary;
private static final Logger logger = LoggerFactory.getLogger(IdentifyReactionsMetabolites.class);
public IdentifyReactionsMetabolites(Map<String, Set<TcNumberContainer2>> reactionsData, BiosynthMetabolites namesAndIDsContainer,
Map<String, BiosynthMetaboliteProperties> allData, BiodbGraphDatabaseService service) {
BiodbGraphDatabaseService service) {
this.dictionary = new Synonyms();
this.allData = allData;