List of usage examples for java.util NavigableMap keySet
Set<K> keySet();
From source file:org.opencb.opencga.storage.hadoop.variant.VariantHbaseDBAdaptor.java
@Override public QueryResult<Variant> getAllVariantsByRegionAndStudy(Region region, String sourceId, QueryOptions options) {/*from www . j a va2s . c om*/ Long start, end, dbstart, dbend; start = System.currentTimeMillis(); QueryResult<Variant> queryResult = new QueryResult<>( String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd())); List<Variant> results = new LinkedList<>(); boolean includeSamples; boolean includeStats; boolean includeEffects; if (!options.containsKey("samples") && !options.containsKey("stats") && !options.containsKey("effects")) { includeSamples = true; includeStats = true; includeEffects = true; } else { includeSamples = options.containsKey("samples") && options.getBoolean("samples"); includeStats = options.containsKey("stats") && options.getBoolean("stats"); includeEffects = options.containsKey("effects") && options.getBoolean("effects"); } try { String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart())); String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd())); HTable table = new HTable(admin.getConfiguration(), tableName); dbstart = System.currentTimeMillis(); Scan regionScan = new Scan(startRow.getBytes(), stopRow.getBytes()); ResultScanner scanres = table.getScanner(regionScan); dbend = System.currentTimeMillis(); queryResult.setDbTime(dbend - dbstart); // Iterate over results and, optionally, their samples and statistics for (Result result : scanres) { String[] rowkeyParts = new String(result.getRow(), CHARSET_UTF_8).split("_"); String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", ""); int position = Integer.parseInt(rowkeyParts[1]); // Get basic result fields from Protocol Buffers message NavigableMap<byte[], byte[]> infoMap = result.getFamilyMap("i".getBytes()); byte[] byteInfo = infoMap.get((sourceId + "_data").getBytes()); VariantFieldsProtos.VariantInfo protoInfo = VariantFieldsProtos.VariantInfo.parseFrom(byteInfo); String reference = protoInfo.getReference(); String alternate = StringUtils.join(protoInfo.getAlternateList(), ","); String format = StringUtils.join(protoInfo.getFormatList(), ":"); Variant variant = new Variant(chromosome, position, position, reference, alternate); // Set samples if requested if (includeSamples) { NavigableMap<byte[], byte[]> sampleMap = result.getFamilyMap("d".getBytes()); Map<String, Map<String, String>> resultSampleMap = new HashMap<>(); // Set samples for (byte[] s : sampleMap.keySet()) { String sampleName = (new String(s, CHARSET_UTF_8)).replaceAll(sourceId + "_", ""); 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]); } // TODO // variant.addSampleData(sampleName, singleSampleMap); } } // Set stats if requested if (includeStats) { byte[] byteStats = infoMap.get((sourceId + "_stats").getBytes()); VariantFieldsProtos.VariantStats protoStats = VariantFieldsProtos.VariantStats .parseFrom(byteStats); VariantStats variantStats = new VariantStats(chromosome, position, reference, alternate, protoStats.getMaf(), protoStats.getMgf(), protoStats.getMafAllele(), protoStats.getMgfGenotype(), protoStats.getMissingAlleles(), protoStats.getMissingGenotypes(), protoStats.getMendelianErrors(), protoStats.getIsIndel(), protoStats.getCasesPercentDominant(), protoStats.getControlsPercentDominant(), protoStats.getCasesPercentRecessive(), protoStats.getControlsPercentRecessive()); variant.setStats(variantStats); } if (includeEffects) { QueryResult<VariantEffect> queryEffects = getEffectsByVariant(variant, options); variant.setEffect(queryEffects.getResult()); } results.add(variant); } } catch (IOException e) { System.err.println(e.getClass().getName() + ": " + e.getMessage()); } queryResult.setResult(results); queryResult.setNumResults(results.size()); end = System.currentTimeMillis(); queryResult.setTime(end - start); return queryResult; }
From source file:org.opencb.opencga.storage.hadoop.variant.VariantHbaseDBAdaptor.java
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);//w ww. j a va 2 s .co m } //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; }
From source file:org.openstreetmap.osmosis.hbase.utility.MockHTable.java
private static List<KeyValue> toKeyValue(byte[] row, NavigableMap<byte[], NavigableMap<byte[], NavigableMap<Long, byte[]>>> rowdata, long timestampStart, long timestampEnd, int maxVersions) { LOG.info("Maxversions: " + maxVersions); List<KeyValue> ret = new ArrayList<KeyValue>(); for (byte[] family : rowdata.keySet()) for (byte[] qualifier : rowdata.get(family).keySet()) { int versionsAdded = 0; //LOG.info("num cells: " + rowdata.get(family).get(qualifier).descendingMap().entrySet().size()); for (Map.Entry<Long, byte[]> tsToVal : rowdata.get(family).get(qualifier).descendingMap() .entrySet()) {// w w w. ja v a 2 s. com if (versionsAdded++ == maxVersions) break; Long timestamp = tsToVal.getKey(); if (timestamp < timestampStart) continue; if (timestamp > timestampEnd) continue; byte[] value = tsToVal.getValue(); ret.add(new KeyValue(row, family, qualifier, timestamp, value)); } } return ret; }