org.opencb.cellbase.lib.builders.RefSeqGeneBuilderIndexer Maven / Gradle / Ivy
/*
* Copyright 2015-2020 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.opencb.cellbase.lib.builders;
import org.apache.commons.lang.StringUtils;
import org.apache.poi.ss.usermodel.*;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;
import org.opencb.biodata.formats.io.FileFormatException;
import org.opencb.biodata.models.core.MirnaTarget;
import org.opencb.biodata.models.core.TargetGene;
import org.opencb.biodata.models.variant.avro.GeneDrugInteraction;
import org.opencb.biodata.models.variant.avro.GeneTraitAssociation;
import org.opencb.commons.utils.FileUtils;
import org.rocksdb.RocksDBException;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.*;
public class RefSeqGeneBuilderIndexer extends GeneBuilderIndexer{
public RefSeqGeneBuilderIndexer(Path refSeqDirectoryPath) {
super(refSeqDirectoryPath);
}
public void index(Path maneFile, Path lrgFile, Path proteinFastaFile, Path cDnaFastaFile, Path geneDrugFile, Path hpoFilePath,
Path disgenetFile, Path miRTarBaseFile, Path cancerGeneGensus, Path cancerHotspot, Path tso500File,
Path eglhHaemOncFile) throws IOException, RocksDBException, FileFormatException {
indexManeMapping(maneFile, "refseq");
indexLrgMapping(lrgFile, "refseq");
indexProteinSequences(proteinFastaFile);
indexCdnaSequences(cDnaFastaFile);
indexDrugs(geneDrugFile);
indexDiseases(hpoFilePath, disgenetFile);
indexMiRTarBase(miRTarBaseFile);
indexCancerGeneCensus(cancerGeneGensus);
indexCancerHotspot(cancerHotspot);
indexTSO500(tso500File);
indexEGLHHaemOnc(eglhHaemOncFile);
}
private void indexDrugs(Path geneDrugFile) throws IOException, RocksDBException {
if (geneDrugFile != null && Files.exists(geneDrugFile) && Files.size(geneDrugFile) > 0) {
logger.info("Loading gene-drug interaction data from '{}'", geneDrugFile);
BufferedReader br = FileUtils.newBufferedReader(geneDrugFile);
// Skip header
br.readLine();
int lineCounter = 1;
String line;
String currentGene = "";
List drugs = new ArrayList<>();
while ((line = br.readLine()) != null) {
String[] parts = line.split("\t");
String geneName = parts[0];
if (currentGene.equals("")) {
currentGene = geneName;
} else if (!currentGene.equals(geneName)) {
rocksDbManager.update(rocksdb, currentGene + DRUGS_SUFFIX, drugs);
drugs = new ArrayList<>();
currentGene = geneName;
}
String source = null;
if (parts.length >= 4) {
source = parts[3];
}
String interactionType = null;
if (parts.length >= 5) {
interactionType = parts[4];
}
String drugName = null;
if (parts.length >= 8) {
// if drug name column is empty, use drug claim name instead
drugName = StringUtils.isEmpty(parts[7]) ? parts[6] : parts[7];
}
if (StringUtils.isEmpty(drugName)) {
// no drug name
continue;
}
String chemblId = null;
if (parts.length >= 9) {
chemblId = parts[8];
}
List publications = new ArrayList<>();
if (parts.length >= 10 && parts[9] != null) {
publications = Arrays.asList(parts[9].split(","));
}
GeneDrugInteraction drug = new GeneDrugInteraction(
geneName, drugName, source, null, null, interactionType, chemblId, publications);
drugs.add(drug);
lineCounter++;
}
br.close();
// update last gene
rocksDbManager.update(rocksdb, currentGene + DRUGS_SUFFIX, drugs);
} else {
logger.warn("Gene drug file " + geneDrugFile + " not found");
logger.warn("Ignoring " + geneDrugFile);
}
}
public List getDrugs(String id) throws RocksDBException, IOException {
String key = id + DRUGS_SUFFIX;
return rocksDbManager.getDrugs(rocksdb, key);
}
private void indexDiseases(Path hpoFilePath, Path disgenetFilePath) throws IOException, RocksDBException {
Map> geneDiseaseAssociationMap = new HashMap<>(50000);
String line;
if (hpoFilePath != null && hpoFilePath.toFile().exists() && Files.size(hpoFilePath) > 0) {
BufferedReader bufferedReader = FileUtils.newBufferedReader(hpoFilePath);
// skip first header line
bufferedReader.readLine();
while ((line = bufferedReader.readLine()) != null) {
String[] fields = line.split("\t");
String omimId = fields[6];
String geneSymbol = fields[3];
String hpoId = fields[0];
String diseaseName = fields[1];
GeneTraitAssociation disease =
new GeneTraitAssociation(omimId, diseaseName, hpoId, 0f, 0, new ArrayList<>(), new ArrayList<>(), "hpo");
addValueToMapElement(geneDiseaseAssociationMap, geneSymbol, disease);
}
bufferedReader.close();
}
if (disgenetFilePath != null && disgenetFilePath.toFile().exists() && Files.size(disgenetFilePath) > 0) {
BufferedReader bufferedReader = FileUtils.newBufferedReader(disgenetFilePath);
// skip first header line
bufferedReader.readLine();
while ((line = bufferedReader.readLine()) != null) {
String[] fields = line.split("\t");
String diseaseId = fields[4];
String diseaseName = fields[5];
String score = fields[9];
String numberOfPubmeds = fields[13].trim();
String numberOfSNPs = fields[14];
String source = fields[15];
GeneTraitAssociation disease = new GeneTraitAssociation(diseaseId, diseaseName, "", Float.parseFloat(score),
Integer.parseInt(numberOfPubmeds), Arrays.asList(numberOfSNPs), Arrays.asList(source), "disgenet");
addValueToMapElement(geneDiseaseAssociationMap, fields[1], disease);
}
bufferedReader.close();
}
for (Map.Entry> entry : geneDiseaseAssociationMap.entrySet()) {
rocksDbManager.update(rocksdb, entry.getKey() + DISEASE_SUFFIX, entry.getValue());
}
}
public List getDiseases(String id) throws RocksDBException, IOException {
String key = id + DISEASE_SUFFIX;
return rocksDbManager.getDiseases(rocksdb, key);
}
private void indexMiRTarBase(Path miRTarBaseFile) throws IOException, RocksDBException {
if (miRTarBaseFile != null && Files.exists(miRTarBaseFile) && Files.size(miRTarBaseFile) > 0) {
logger.info("Loading mirna targets from '{}'", miRTarBaseFile);
FileInputStream file = new FileInputStream(miRTarBaseFile.toFile());
Workbook workbook = new XSSFWorkbook(file);
Sheet sheet = workbook.getSheetAt(0);
Iterator iterator = sheet.iterator();
String currentMiRTarBaseId = null;
String currentMiRNA = null;
String currentGene = null;
List targetGenes = new ArrayList();
Map> geneToMirna = new HashMap();
while (iterator.hasNext()) {
Row currentRow = iterator.next();
Iterator cellIterator = currentRow.iterator();
Cell cell = cellIterator.next();
String miRTarBaseId = cell.getStringCellValue();
// skip header
if (miRTarBaseId.startsWith("miRTarBase")) {
continue;
}
if (currentMiRTarBaseId == null) {
currentMiRTarBaseId = miRTarBaseId;
}
cell = cellIterator.next();
String miRNA = cell.getStringCellValue();
if (currentMiRNA == null) {
currentMiRNA = miRNA;
}
// species
cellIterator.next();
cell = cellIterator.next();
String geneName = cell.getStringCellValue();
if (currentGene == null) {
currentGene = geneName;
}
// entrez
cellIterator.next();
// species
cellIterator.next();
if (!miRTarBaseId.equals(currentMiRTarBaseId) || !geneName.equals(currentGene)) {
// new entry, store current one
MirnaTarget miRnaTarget = new MirnaTarget(currentMiRTarBaseId, "miRTarBase", currentMiRNA,
targetGenes);
addValueToMapElement(geneToMirna, currentGene, miRnaTarget);
targetGenes = new ArrayList();
currentGene = geneName;
currentMiRTarBaseId = miRTarBaseId;
currentMiRNA = miRNA;
}
// experiment
cell = cellIterator.next();
String experiment = cell.getStringCellValue();
// support type
cell = cellIterator.next();
String supportType = cell.getStringCellValue();
// pubmeds
cell = cellIterator.next();
String pubmed = null;
// seems to vary, so check both
if (cell.getCellType().equals(CellType.NUMERIC)) {
pubmed = String.valueOf(cell.getNumericCellValue());
} else {
pubmed = cell.getStringCellValue();
}
targetGenes.add(new TargetGene(experiment, supportType, pubmed));
}
// parse last entry
MirnaTarget miRnaTarget = new MirnaTarget(currentMiRTarBaseId, "miRTarBase", currentMiRNA,
targetGenes);
addValueToMapElement(geneToMirna, currentGene, miRnaTarget);
for (Map.Entry> entry : geneToMirna.entrySet()) {
rocksDbManager.update(rocksdb, entry.getKey() + MIRTARBASE_SUFFIX, entry.getValue());
}
} else {
logger.error("mirtarbase file not found");
}
}
public List getMirnaTargets(String geneName) throws RocksDBException, IOException {
String key = geneName + MIRTARBASE_SUFFIX;
return rocksDbManager.getMirnaTargets(rocksdb, key);
}
private static void addValueToMapElement(Map> map, String key, T value) {
if (map.containsKey(key)) {
map.get(key).add(value);
} else {
List valueList = new ArrayList<>();
valueList.add(value);
map.put(key, valueList);
}
}
}
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