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Commit 114d7a92 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

small bug fixed

parent 0d1f86a7
......@@ -5,7 +5,7 @@
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>scraper</artifactId>
<version>0.0.10-SNAPSHOT</version>
<version>0.0.11-SNAPSHOT</version>
<packaging>jar</packaging>
<name>scraper</name>
......@@ -66,7 +66,7 @@
<dependency>
<groupId>pt.uminho.ceb.biosystems.transyt</groupId>
<artifactId>utilities</artifactId>
<version>0.0.10-SNAPSHOT</version>
<version>0.0.11-SNAPSHOT</version>
</dependency>
<dependency>
......
......@@ -43,7 +43,7 @@ public class GenerateTransportReactions {
// Map<String, TcdbMetabolitesContainer> tcdbMetabolites2 = new HashMap<>();
//
// tcdbMetabolites2.put("P0ABB0", tcdbMetabolites.get("P0ABB0"));
// tcdbMetabolites2.put("P29707", tcdbMetabolites.get("P29707"));
for(String accession : tcdbMetabolites.keySet()) {
......@@ -52,6 +52,9 @@ public class GenerateTransportReactions {
TcdbMetabolitesContainer tcdbMetContainer = tcdbMetabolites.get(accession);
for(String tcNumber : tcdbMetContainer.getTcNumbers()) {
// if(tcNumber.contains("2.A.4."))
// System.out.println(tcNumber);
// System.out.println(tcNumber);
......@@ -1936,7 +1939,7 @@ public class GenerateTransportReactions {
try {
if(proteinDescription.matches("(?i).*uptake[\\s*\\.*]*.*") || proteinDescription.matches("(?i).*enter[\\s*\\.*]*.*")
if(proteinDescription.matches("(?i).*uptake[\\s*\\.*]*.*")
|| proteinDescription.matches("(?i).*import[\\s*\\.*]*.*"))
return true;
......
......@@ -11,6 +11,7 @@ import pt.uminho.ceb.biosystems.transyt.scraper.tcdb.reactionsGenerator.Generate
import pt.uminho.ceb.biosystems.transyt.scraper.tcdb.utilities.ProcessTcdbMetabolitesExcel;
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.connection.ReadFastaTcdb;
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.files.FilesUtils;
......@@ -21,12 +22,10 @@ public class Retriever {
private static final Logger logger = LoggerFactory.getLogger(Retriever.class);
public static void main(String[] args) throws Exception {
public static void runRetriever(boolean useCache) throws Exception {
try {
boolean useCache = false;
///////// - SEARCHER
logger.info("Retrieving TCDB FASTA file...");
......@@ -34,7 +33,9 @@ public class Retriever {
if(!useCache)
TcdbRetriever.getSubstrates();
Set<String> tcNumbers = TcdbExplorer.getTcNumbers(useCache);
ReadFastaTcdb.buildFastaFileForAlignments();
Set<String> tcNumbers = TcdbExplorer.getTcNumbers(true);
Set<String> toSearch = TcdbExplorer.generateTCsFamily(tcNumbers);
......@@ -52,7 +53,6 @@ public class Retriever {
//////////
logger.info("Search complete!");
......
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