@Override
protected void setup(Context context) throws IOException, InterruptedException {
super.setup(context);
setupGCBins(context.getConfiguration());
genomeAdmin = HBaseGenomeAdmin.getHBaseGenomeAdmin(context.getConfiguration());
variationAdmin = VariationAdmin.getInstance(context.getConfiguration());
genomeName = context.getConfiguration().get("genome");
parentGenome = context.getConfiguration().get("parent");
genome = genomeAdmin.getGenomeTable().getGenome(genomeName);
if (genome == null) throw new IOException("Genome " + genome + " is missing.");
try {
SNVProbability table =
(SNVProbability) variationAdmin.getTable(VariationTables.SNVP.getTableName());
snvProbabilities = table.getProbabilities();
SizeProbability sizeTable =
(SizeProbability) variationAdmin.getTable(VariationTables.SIZE.getTableName());
sizeProbabilities = sizeTable.getProbabilities();
variationList = sizeTable.getVariationList();
variationList.add("SNV");
} catch (ProbabilityException e) {
throw new InterruptedException("Failed to start mapper: " + e);
}
varTable = (VariationCountPerBin) variationAdmin.getTable(VariationTables.VPB.getTableName());
}
@Override
protected void map(ImmutableBytesWritable key, Result value, Context context)
throws IOException, InterruptedException {
if (maxGCBins == null || GCBins == null) throw new IOException("GC Bins need to be set up.");
long start = System.currentTimeMillis();
final SequenceResult origSeq = genomeAdmin.getSequenceTable().createResult(value);
final ChromosomeResult origChr =
genomeAdmin.getChromosomeTable().getChromosome(parentGenome, origSeq.getChr());
// get hbase objects for new genome
ChromosomeResult mutatedChr =
genomeAdmin.getChromosomeTable().getChromosome(genome.getName(), origSeq.getChr());
if (mutatedChr == null) {
String rowId =
genomeAdmin
.getChromosomeTable()
.addChromosome(
genome, origChr.getChrName(), origChr.getLength(), origChr.getSegmentNumber());
mutatedChr = genomeAdmin.getChromosomeTable().queryTable(rowId);
}
/* --- Mutate sequence --- */
Random randomFragment = new Random();
DNASequence mutatedSequence = new DNASequence(origSeq.getSequence());
/* Don't bother to try and mutate a fragment that is more than 70% 'N' */
int gcContent = mutatedSequence.calculateGC();
if (gcContent > (0.3 * origSeq.getSequenceLength())) {
GCBin.GCResult gcResult = maxGCBins.get(origSeq.getChr());
if (gcContent < gcResult.getMax()) getBin(origSeq.getChr(), gcContent);
// get random fragment within this bin
List<VCPBResult> varsPerFrag =
varTable.getFragment(
origSeq.getChr(),
gcResult.getMin(),
gcResult.getMax(),
randomFragment.nextInt(gcResult.getTotalFragments()),
variationList);
Map<Variation, Map<Location, DNASequence>> mutations =
new HashMap<Variation, Map<Location, DNASequence>>();
// apply the variations to the sequence, each of them needs to apply to the same fragment
// it is possible that one could override another (e.g. a deletion removes SNVs)
// TODO need to check that these are ordered these by variation based on the hbase
// ordering...SNV, del, ins, ...
for (VCPBResult variation : varsPerFrag) {
Variation v = createInstance(variation.getVariationClass());
v.setVariationName(variation.getVariationName());
if (variation.getVariationName().equals("SNV")) {
SNV snv = ((SNV) v);
snv.setSnvFrequencies(snvProbabilities);
} else v.setSizeVariation(sizeProbabilities.get(variation.getVariationName()));
mutatedSequence = v.mutateSequence(mutatedSequence, variation.getVariationCount());
if (v.getLastMutations().size() > 0) mutations.put(v, v.getLastMutations());
}
String mutSeqRowId =
genomeAdmin
.getSequenceTable()
.addSequence(
mutatedChr,
origSeq.getStart(),
(origSeq.getStart() + mutatedSequence.getLength()),
mutatedSequence.getSequence(),
origSeq.getSegmentNum());
if (mutSeqRowId == null) throw new IOException("Failed to add sequence.");
// add any mutations to the small mutations table, best done as a batch job
List<Put> puts = new ArrayList<Put>();
SequenceResult mutSequence = genomeAdmin.getSequenceTable().queryTable(mutSeqRowId);
for (Variation v : mutations.keySet()) {
for (Map.Entry<Location, DNASequence> entry : mutations.get(v).entrySet()) {
try {
Row row =
genomeAdmin
.getSmallMutationsTable()
.newMutationRow(
mutSequence,
v,
entry.getKey().getStart(),
entry.getKey().getEnd(),
entry.getValue().getSequence());
puts.add(new Put(genomeAdmin.getSmallMutationsTable().getPut(row)));
} catch (IllegalArgumentException ae) {
log.error("Failed to add " + mutSeqRowId + " var " + v.toString(), ae);
}
}
}
try {
genomeAdmin.getSmallMutationsTable().put(puts);
} catch (IOException ioe) {
log.error(ioe);
}
} else
genomeAdmin
.getSequenceTable()
.addSequence(
mutatedChr,
origSeq.getStart(),
origSeq.getEnd(),
origSeq.getSequence(),
origSeq.getSegmentNum());
long end = System.currentTimeMillis() - start;
log.debug("FINISHED MAP " + origSeq.getRowId() + " time=" + String.valueOf(end));
}
