public List<Variant> getRecordSimpleStats( String study, int missing_gt, float maf, String maf_allele) { BasicDBObject compare = new BasicDBObject("studies.stats.allele_maf", maf_allele) .append("studies.stats.MAF", maf) .append("studies.stats.missing", missing_gt); List<Get> hbaseQuery = new ArrayList<>(); DBCollection collection = db.getCollection("variants"); Iterator<DBObject> result = collection.find(compare); String chromosome = new String(); while (result.hasNext()) { DBObject variant = result.next(); String position = variant.get("_id").toString(); // hbase query construction Get get = new Get(position.getBytes()); hbaseQuery.add(get); } // Complete results, from HBase tableName = study; effectTableName = tableName + "effect"; Map<String, Variant> resultsMap = new HashMap<>(); try { HTable table = new HTable(admin.getConfiguration(), tableName); HTable effectTable = new HTable(admin.getConfiguration(), effectTableName); Result[] hbaseResultEffect = effectTable.get(hbaseQuery); Result[] hbaseResultStats = table.get(hbaseQuery); // List<Variant> results = new LinkedList<>(); for (Result r : hbaseResultStats) { String position = new String(r.getRow(), CHARSET_UTF_8); String[] aux = position.split("_"); String inner_position = aux[1]; String chr = aux[0]; // position parsing if (chr.startsWith("0")) { chr = chr.substring(1); } while (inner_position.startsWith("0")) { inner_position = inner_position.substring(1); } List<VariantFieldsProtos.VariantSample> samples = new LinkedList<>(); NavigableMap<byte[], byte[]> infoMap = r.getFamilyMap("i".getBytes()); byte[] byteStats = infoMap.get((study + "_stats").getBytes()); VariantFieldsProtos.VariantStats stats = VariantFieldsProtos.VariantStats.parseFrom(byteStats); byte[] byteInfo = infoMap.get((study + "_data").getBytes()); VariantFieldsProtos.VariantInfo info = VariantFieldsProtos.VariantInfo.parseFrom(byteInfo); String alternate = StringUtils.join(info.getAlternateList(), ", "); String reference = info.getReference(); Variant partialResult = new Variant( chr, Integer.parseInt(inner_position), Integer.parseInt(inner_position), reference, alternate); String format = StringUtils.join(info.getFormatList(), ":"); NavigableMap<byte[], byte[]> sampleMap = r.getFamilyMap("d".getBytes()); Map<String, Map<String, String>> resultSampleMap = new HashMap<>(); // StringBuilder sampleRaw = new StringBuilder(); for (byte[] s : sampleMap.keySet()) { String qual = (new String(s, CHARSET_UTF_8)).replaceAll(study + "_", ""); VariantFieldsProtos.VariantSample sample = VariantFieldsProtos.VariantSample.parseFrom(sampleMap.get(s)); String sample1 = sample.getSample(); String[] values = sample1.split(":"); String[] fields = format.split(":"); Map<String, String> singleSampleMap = new HashMap<>(); for (int i = 0; i < fields.length; i++) { singleSampleMap.put(fields[i], values[i]); } resultSampleMap.put(qual, singleSampleMap); } VariantStats variantStats = new VariantStats( chromosome, Integer.parseInt(inner_position), reference, alternate, stats.getMaf(), stats.getMgf(), stats.getMafAllele(), stats.getMgfGenotype(), stats.getMissingAlleles(), stats.getMissingGenotypes(), stats.getMendelianErrors(), stats.getIsIndel(), stats.getCasesPercentDominant(), stats.getControlsPercentDominant(), stats.getCasesPercentRecessive(), stats.getControlsPercentRecessive()); partialResult.setStats(variantStats); resultsMap.put(new String(r.getRow(), CHARSET_UTF_8), partialResult); } for (Result r : hbaseResultEffect) { if (!r.isEmpty()) { NavigableMap<byte[], byte[]> effectMap = r.getFamilyMap("e".getBytes()); Variant partialResult = resultsMap.get(new String(r.getRow(), CHARSET_UTF_8)); System.out.println("Recuperado " + partialResult.toString()); String s = partialResult.getReference() + "_" + partialResult.getAlternate(); VariantEffectProtos.EffectInfo effectInfo = VariantEffectProtos.EffectInfo.parseFrom(effectMap.get(s.getBytes())); VariantEffect variantEffect = new VariantEffect( partialResult.getChromosome(), (int) partialResult.getStart(), partialResult.getReference(), partialResult.getAlternate(), effectInfo.getFeatureId(), effectInfo.getFeatureName(), effectInfo.getFeatureType(), effectInfo.getFeatureBiotype(), effectInfo.getFeatureChromosome(), effectInfo.getFeatureStart(), effectInfo.getFeatureEnd(), effectInfo.getFeatureStrand(), effectInfo.getSnpId(), effectInfo.getAncestral(), effectInfo.getAlternative(), effectInfo.getGeneId(), effectInfo.getTranscriptId(), effectInfo.getGeneName(), effectInfo.getConsequenceType(), effectInfo.getConsequenceTypeObo(), effectInfo.getConsequenceTypeDesc(), effectInfo.getConsequenceTypeType(), effectInfo.getAaPosition(), effectInfo.getAminoacidChange(), effectInfo.getCodonChange()); resultsMap.put(new String(r.getRow(), CHARSET_UTF_8), partialResult); } } } catch (InvalidProtocolBufferException e) { System.err.println(e.getClass().getName() + ": " + e.getMessage()); } catch (IOException e) { System.err.println(e.getClass().getName() + ": " + e.getMessage()); } List<Variant> results = new ArrayList<>(resultsMap.values()); return results; }
public QueryResult getSimpleVariantsByRegion( Region region, String sourceId, QueryOptions options) { Long start, end, dbstart, dbend; start = System.currentTimeMillis(); boolean includeStats; boolean includeEffects; if (!options.containsKey("stats") && !options.containsKey("effects")) { includeStats = true; includeEffects = true; } else { includeStats = options.containsKey("stats") && options.getBoolean("stats"); includeEffects = options.containsKey("effects") && options.getBoolean("effects"); } QueryResult<Variant> queryResult = new QueryResult<>( String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd())); List<Variant> results = new ArrayList<>(); String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart())); String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd())); BasicDBObject query = new BasicDBObject("position", new BasicDBObject("$gte", startRow).append("$lte", stopRow)) .append("sources.sourceId", sourceId); DBCollection collection = db.getCollection("variants"); dbstart = System.currentTimeMillis(); DBCursor variantInStudies = collection.find(query); dbend = System.currentTimeMillis(); queryResult.setDbTime(dbend - dbstart); for (DBObject result : variantInStudies) { String[] rowkeyParts = result.get("position").toString().split("_"); String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", ""); int position = Integer.parseInt(rowkeyParts[1]); BasicDBList studies = (BasicDBList) result.get("sources"); BasicDBObject st = (BasicDBObject) studies.get(0); String ref = (String) st.get("ref"); String alt = StringUtils.join((ArrayList<String>) st.get("alt"), ","); // TODO Needs rework Variant variant = new Variant(chromosome, position, position, ref, alt); // Set stats informations if (includeStats) { VariantStats stats = new VariantStats(); BasicDBObject mongoStats = (BasicDBObject) st.get("stats"); stats.setMaf((float) (double) mongoStats.get("maf")); stats.setMafAllele((String) mongoStats.get("alleleMaf")); stats.setMissingGenotypes((int) mongoStats.get("missing")); List<Genotype> genotypeCount = new ArrayList<>(); for (BasicDBObject s : (List<BasicDBObject>) mongoStats.get("genotypeCount")) { for (Map.Entry<String, Object> entry : s.entrySet()) { Genotype genotype = new Genotype(entry.getKey()); genotype.setCount((Integer) entry.getValue()); genotypeCount.add(genotype); } } stats.setGenotypes(genotypeCount); variant.setStats(stats); } // TODO Set consequence type names if (includeEffects) { BasicDBList mongoEffects = (BasicDBList) st.get("effects"); if (mongoEffects != null) { for (Object e : mongoEffects) { String effectObo = e.toString(); VariantEffect effect = new VariantEffect(); effect.setConsequenceTypeObo(effectObo); variant.addEffect(effect); } } } results.add(variant); } queryResult.setResult(results); queryResult.setNumResults(results.size()); end = System.currentTimeMillis(); queryResult.setTime(end - start); return queryResult; }