/**
* Create a string to serialize to a file
*
* @return
*/
@SuppressWarnings("unchecked")
@Override
public String serializeSave(MarkerSerializer markerSerializer) {
return super.serializeSave(markerSerializer) //
+ "\t"
+ markerSerializer.save((Collection<Marker>) subIntervals.values()) //
;
}
/** Parse a line from a serialized file */
@SuppressWarnings("unchecked")
@Override
public void serializeParse(MarkerSerializer markerSerializer) {
super.serializeParse(markerSerializer);
Markers markers = markerSerializer.getNextFieldMarkers();
for (Marker m : markers) add((T) m);
}
/** Load predictor from a binary file */
public static SnpEffectPredictor load(Config config) {
String snpEffPredFile = config.getFileSnpEffectPredictor();
// Sanity check
if (!Gpr.canRead(snpEffPredFile))
throw new RuntimeException(
"\tERROR: Cannot read file '"
+ snpEffPredFile
+ "'.\n\tYou can try to download the database by running the following command:\n\t\tjava -jar snpEff.jar download "
+ config.getGenome().getVersion()
+ "\n");
// Load markers from file
MarkerSerializer ms = new MarkerSerializer();
Markers markers = ms.load(snpEffPredFile);
// Find genome
Genome genome = null;
for (Marker m : markers) if (m instanceof Genome) genome = (Genome) m;
if (genome == null) throw new RuntimeException("Genome not found. This should never happen!");
// Create predictor
SnpEffectPredictor snpEffectPredictor = new SnpEffectPredictor(genome);
// Add genes
for (Marker m : markers)
if (m instanceof Gene) {
Gene gene = (Gene) m;
snpEffectPredictor.add(gene);
}
// Add 'other' markers
for (Marker m : markers)
if (!(m instanceof Genome) //
&& !(m instanceof Chromosome) //
&& !(m instanceof Gene) //
&& !(m instanceof Transcript) //
&& !(m instanceof Exon) //
&& !(m instanceof Cds) //
&& !(m instanceof Utr) //
&& !(m instanceof SpliceSite) //
) snpEffectPredictor.add(m);
return snpEffectPredictor;
}
/** Save nextprot markers */
void save() {
String nextProtBinFile = config.getDirDataVersion() + "/nextProt.bin";
if (verbose) Timer.showStdErr("Saving database to file '" + nextProtBinFile + "'");
// Add chromosomes
HashSet<Chromosome> chromos = new HashSet<Chromosome>();
for (Marker m : markers) chromos.add(m.getChromosome());
// Create a set of all markers to be saved
Markers markersToSave = new Markers();
markersToSave.add(genome);
for (Chromosome chr : chromos) markersToSave.add(chr);
for (Marker m : markers) markersToSave.add(m);
// Save
MarkerSerializer markerSerializer = new MarkerSerializer();
markerSerializer.save(nextProtBinFile, markersToSave);
}
/** Save predictor to a binary file (specified by the configuration) */
public void save(Config config) {
String databaseFile = config.getFileSnpEffectPredictor();
MarkerSerializer markerSerializer = new MarkerSerializer();
markerSerializer.save(databaseFile, this);
}