private Map<String, List<GeneDrugInteraction>> getGeneDrugMap() throws IOException { Map<String, List<GeneDrugInteraction>> geneDrugMap = new HashMap<>(); BufferedReader br; if (geneDrugFile.toFile().getName().endsWith(".gz")) { br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(geneDrugFile.toFile())))); } else { br = Files.newBufferedReader(geneDrugFile, Charset.defaultCharset()); } logger.info("Loading gene-drug data form {}", geneDrugFile); // Skip header br.readLine(); int lineCounter = 1; String line; while ((line = br.readLine()) != null) { String[] parts = line.split("\t"); addValueToMapElement(geneDrugMap, parts[0], new GeneDrugInteraction(parts[0], parts[4], "dgidb", parts[2], parts[3])); lineCounter++; } br.close(); return geneDrugMap; }
if (geneDrugInteractionList != null) { for (GeneDrugInteraction geneDrugInteraction : geneDrugInteractionList) { Document drugDbObject = new Document(DRUG_GENE_FIELD, geneDrugInteraction.getGeneName()); putNotNull(drugDbObject, DRUG_NAME_FIELD, geneDrugInteraction.getDrugName()); putNotDefault(drugDbObject, DRUG_SOURCE_FIELD, geneDrugInteraction.getSource(), DEFAULT_DRUG_SOURCE); putNotNull(drugDbObject, DRUG_STUDY_TYPE_FIELD, geneDrugInteraction.getStudyType()); putNotDefault(drugDbObject, DRUG_TYPE_FIELD, geneDrugInteraction.getType(), DEFAULT_DRUG_TYPE); drugGeneInteractions.add(drugDbObject);
@Test public void testGetAllVariants_drugs() { //ANNOT_DRUG Query query; Map<String, Integer> drugs = new HashMap<>(); for (Variant variant : allVariants.getResult()) { if (variant.getAnnotation().getGeneDrugInteraction() != null) { Set<String> drugsInVariant = new HashSet<>(); for (GeneDrugInteraction drugInteraction : variant.getAnnotation().getGeneDrugInteraction()) { drugsInVariant.add(drugInteraction.getDrugName()); } for (String flag : drugsInVariant) { drugs.put(flag, drugs.getOrDefault(flag, 0) + 1); } } } int i = 0; for (Map.Entry<String, Integer> entry : drugs.entrySet()) { if (entry.getKey().contains(",")) { continue; } query = new Query(ANNOT_DRUG.key(), entry.getKey()); queryResult = query(query, null); assertEquals(entry.getKey(), entry.getValue().intValue(), queryResult.getNumResults()); if (++i > QUERIES_LIM) { break; } } }
addNotNull(drugs, drug.getDrugName());
public static Map<String, List<GeneDrugInteraction>> getGeneDrugMap(Path geneDrugFile) throws IOException { Map<String, List<GeneDrugInteraction>> geneDrugMap = new HashMap<>(); 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; while ((line = br.readLine()) != null) { String[] parts = line.split("\t"); addValueToMapElement(geneDrugMap, parts[0], new GeneDrugInteraction(parts[0], parts[4], "dgidb", parts[2], parts[3])); lineCounter++; } br.close(); } else { logger.warn("Gene drug file " + geneDrugFile + " not found"); logger.warn("Ignoring " + geneDrugFile); } return geneDrugMap; }
@Override public GeneDrugInteraction build() { try { GeneDrugInteraction record = new GeneDrugInteraction(); record.geneName = fieldSetFlags()[0] ? this.geneName : (java.lang.String) defaultValue(fields()[0]); record.drugName = fieldSetFlags()[1] ? this.drugName : (java.lang.String) defaultValue(fields()[1]); record.source = fieldSetFlags()[2] ? this.source : (java.lang.String) defaultValue(fields()[2]); record.studyType = fieldSetFlags()[3] ? this.studyType : (java.lang.String) defaultValue(fields()[3]); record.type = fieldSetFlags()[4] ? this.type : (java.lang.String) defaultValue(fields()[4]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
for (Document dbObject : list) { drugs.add(new GeneDrugInteraction( getDefault(dbObject, DRUG_GENE_FIELD, ""), getDefault(dbObject, DRUG_NAME_FIELD, ""),