/* (non-Javadoc)
* @see org.genomesmanager.services.impl.snps.SnpsImporter#parseMipsSnps(java.util.List)
*/
@Override
public void parseMipsSnps(List<String> lines) {
System.out.println("Lines: " + lines.size());
int lineN = 1;
for (String line : lines) {
String[] elems = line.split("\t+");
String scaffoldName = elems[0];
Sequence seq = sequenceRepository.findLatest(scaffoldName);
if (seq == null) {
errors.add(lineN + "\t" + line + "\t" + "Scaffold " + scaffoldName + " not found");
continue;
}
int pos = Integer.parseInt(elems[1]);
String referenceNucl = elems[2];
for (int i = 3; i < elems.length; i++) {
String reseq = elems[i];
if (!reseq.equals("?")) {
Snp snp = new Snp();
snp.setIndividual(individuals.get(i - 3));
snp.setPos(pos);
snp.setSequence(seq);
snp.setReference(referenceNucl);
snp.setReseq(reseq);
snps.add(snp);
}
}
if (lineN % 1000 == 0) {
System.out.println("Done " + lineN + " of " + lines.size());
}
lineN++;
}
}
@Test
public void test() {
Species sp = SpeciesOM.Generate(1).get(0);
speciesRepo.save(sp);
Chromosome chr = ChromosomesOM.Generate(1, sp).get(0);
chromosomeRepo.save(chr);
Sequence seq = SequencesOM.Generate(1, chr).get(0);
sequenceRepo.save(seq);
Variety variety = VarietiesOM.Generate(1, sp).get(0);
varietyRepo.save(variety);
Individual individual = IndividualsOM.Generate(1, variety).get(0);
individualRepo.save(individual);
Snp snp = SnpsOM.Generate(1, individual, seq).get(0);
snp = snpRepo.save(snp);
Snp postSnp = snpRepo.findOne(snp.getId());
assertEquals(snp, postSnp);
}
@Test
public void testGetAll() {
int nOfSnps = 7;
Species sp = SpeciesOM.Generate(1).get(0);
sp = speciesRepo.save(sp);
Chromosome chr = ChromosomesOM.Generate(1, sp).get(0);
chr = chromosomeRepo.save(chr);
Sequence seq = SequencesOM.Generate(1, chr).get(0);
seq = sequenceRepo.save(seq);
Variety variety = VarietiesOM.Generate(1, sp).get(0);
variety = varietyRepo.save(variety);
Individual individual = IndividualsOM.Generate(1, variety).get(0);
individual = individualRepo.save(individual);
for (Snp snp : SnpsOM.Generate(nOfSnps, individual, seq)) {
snp = snpRepo.save(snp);
}
assertEquals(nOfSnps, snpRepo.getAllByChromosome(chr).size());
assertEquals(nOfSnps, snpRepo.getAllBySpecies(sp).size());
}