diff --git a/docker-compose.yml b/docker-compose.yml
index e3b91868a8b86d5c6102de6b305428281d21b68e..6f9f5f1d3a5baca14a7e7900b572971c16b50263 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -12,26 +12,6 @@ services:
- postgres:/data/postgres
ports:
- 5432:5432
- pgadmin:
- image: dpage/pgadmin4
- depends_on:
- - postgres
- environment:
- PGADMIN_DEFAULT_EMAIL: ${PGADMIN_DEFAULT_EMAIL:-pgadmin4@pgadmin.org}
- PGADMIN_DEFAULT_PASSWORD: ${PGADMIN_DEFAULT_PASSWORD:-password}
- volumes:
- - pgadmin:/root/.pgadmin
- ports:
- - 5050:80
-
- adminer:
- image: adminer
- depends_on:
- - postgres
- environment:
- ADMINER_DEFAULT_SERVER: postgres
- ports:
- - 5000:8080
volumes:
postgres:
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgRepository.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgRepository.java
index 39d7bdcfea00ab067b9a5aff7d971d55dd229044..7291d7ac4758db39654058de4ab09ddc6e073c95 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgRepository.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgRepository.java
@@ -18,7 +18,7 @@ public interface CpgRepository extends BaseRepository<Cpg, UUID> {
@Query("select a from Cpg as a join a.owner o join a.tags t where t = :tag and o.id = ?#{principal.id}")
Page<Cpg> findAll(Pageable pageable, @Param("tag") String tag);
- @Query("select a from Cpg as a join a.owner o where a.id = :id and o.id = ?#{principal.id}")
+ @Query("select a from Cpg a where a.id = :id")
Optional<Cpg> findById(@Param("id") UUID id);
@Query("select distinct t from Cpg as s join s.owner o join s.tags t where o.id = ?#{principal.id}")
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgService.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgService.java
index 6c012e81d2be1a792cd7ada277ddb736deaf7894..9011e9c3c68d117165910fd76d88f2fc4c413534 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgService.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/cpg/CpgService.java
@@ -1,14 +1,10 @@
package cz.mendelu.dnaAnalyser.analyse.cpg;
-import cz.mendelu.dnaAnalyser.analyse.zdna.Zdna;
-import cz.mendelu.dnaAnalyser.analyse.zdna.ZdnaAnalyseResult;
-import cz.mendelu.dnaAnalyser.analyse.zdna.ZdnaMapper;
+
import cz.mendelu.dnaAnalyser.batch.BatchService;
import cz.mendelu.dnaAnalyser.sequence.Sequence;
import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
import cz.mendelu.dnaAnalyser.sequence.data.SequenceDataRepository;
-import cz.mendelu.dnaAnalyser.sequence.stream.BufferedWindow;
-import cz.mendelu.dnaAnalyser.sequence.stream.Window;
import cz.mendelu.dnaAnalyser.utils.analyse.service.heatmap.Heatmap;
import cz.mendelu.dnaAnalyser.utils.exception.NotFoundException;
import cz.mendelu.dnaAnalyser.utils.repository.BaseRepository;
@@ -143,7 +139,7 @@ public class CpgService extends ModelService<Cpg> {
.mapToInt(e -> e.length)
.sum();
- result = analysisCpg.size() != 0
+ result = !analysisCpg.isEmpty()
? totalCpgLen / analysisCpg.size()
: 0;
}
@@ -157,4 +153,9 @@ public class CpgService extends ModelService<Cpg> {
if (!orderIterator.hasNext()) return null;
return orderIterator.next();
}
+
+ public Cpg findOne(UUID id) {
+ return cpgRepository.findById(id)
+ .orElseThrow(() -> new NotFoundException(Cpg.class, id));
+}
}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/exporter/ExporterService.java b/src/main/java/cz/mendelu/dnaAnalyser/exporter/ExporterService.java
index 191b6fa0809e4ec862a14d434def2f9e16c9547c..08bb9b0311a4b1d40a9d096a3c2c96ba2d2327cd 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/exporter/ExporterService.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/exporter/ExporterService.java
@@ -1,8 +1,9 @@
package cz.mendelu.dnaAnalyser.exporter;
import com.opencsv.CSVWriter;
+import cz.mendelu.dnaAnalyser.analyse.cpg.CpgDataSessionService;
+import cz.mendelu.dnaAnalyser.analyse.cpg.CpgService;
import cz.mendelu.dnaAnalyser.utils.analyse.service.AbstractDataSessionService;
-import cz.mendelu.dnaAnalyser.utils.exception.NotFoundException;
import cz.mendelu.dnaAnalyser.analyse.g4hunter.quadruplex.QuadruplexDataSessionService;
import cz.mendelu.dnaAnalyser.analyse.rloopr.RloopDataSessionService;
import org.springframework.beans.factory.annotation.Autowired;
@@ -41,6 +42,11 @@ public class ExporterService {
@Autowired
private AnalyseRepository analyseRepository;
+ @Autowired
+ private CpgDataSessionService cpgDataSessionService;
+
+ @Autowired
+ private CpgService cpgService;
public String exportData(UUID id, Analysis analysis, Output format) {
@@ -65,6 +71,9 @@ public class ExporterService {
case RLOOP:
sessionService = rloopDataSessionService;
break;
+ case CPG:
+ sessionService = cpgDataSessionService;
+ break;
default:
// default to quadruplex for now
sessionService = quadruplexDataSessionService;
@@ -119,6 +128,13 @@ public class ExporterService {
ArrayList<String> zdnaColumns = new ArrayList<>();
zdnaColumns.add("SCORE");
+
+ ArrayList<String> cpxColumns = new ArrayList<>();
+ cpxColumns.add("GCPERC");
+ cpxColumns.add("OBSERVEDTOEXPECTEDCPG");
+ cpxColumns.add("LENGTH");
+
+
String browserHeader = "browser position ";
String result = "track type=bedGraph name=\"%s\" " +
"description=%s " +
@@ -135,7 +151,7 @@ public class ExporterService {
Integer posInGenomeStart = 0;
Integer posInGenomeEnd = 0;
- final String format = "%s %d %d %s\n";
+ String format = "%s %d %d %s\n";
String chrom = getChromName(id);
Pattern p = Pattern.compile("[A-Z][a-z].*_(chr[1-9XY]+):([0-9].+)-([0-9].+)"); // genome browser format, e.g. Human_chr8:128748315-128753680
@@ -175,6 +191,18 @@ public class ExporterService {
analysisColumnMapper = zdnaColumns;
break;
+ case CPG:
+ // Retrieve the second nucleotide from the Cpg service
+ Character secondNuc = cpgService.findOne(id).getSecondNucleotide();
+
+ // Set name and description based on the second nucleotide
+ name = "Cp" + (secondNuc != null ? secondNuc : "X") + " tracker";
+ description = "\"BedGraph output of Cp" + (secondNuc != null ? secondNuc : "X") + " analysis\"";
+
+ // Set the analysisColumnMapper based on the case
+ analysisColumnMapper = cpxColumns;
+ break;
+
default:
name = "";
description = "";
@@ -196,6 +224,9 @@ public class ExporterService {
String strand = null;
int score = 0;
+ double gcperc = 0.0;
+ double observertoexpected = 0.0;
+ int length = 0;
if (analysis == Analysis.RLOOP) {
strand = rs.getString("STRAND");
@@ -214,9 +245,18 @@ public class ExporterService {
score = (int) Math.ceil(rs.getDouble("SCORE") * 100);
} else if (analysis == Analysis.ZDNA) {
score = (int) Math.ceil(rs.getDouble("SCORE"));
+ } else if (analysis == Analysis.CPG) {
+ gcperc = rs.getDouble("gcPerc");
+ observertoexpected = rs.getDouble("observedToExpectedCpG");
+ length = rs.getInt("length");
+ }
+
+ if (analysis == Analysis.CPG) {
+ dataValue = String.format(" %.3f %.3f %d", gcperc*100, observertoexpected, length);
+ } else {
+ dataValue = String.format(" %d", score);
}
- dataValue = String.format(" %d", score);
} catch (SQLException e) {
log.error("Error fetching analysis data: {}", e);