Exemplos de Test_getStandardSlice em C++ (Cpp)

Exemplo n.º 1

int main(int argc, char *argv[]) {
  DBAdaptor *dba;
  RepeatFeatureAdaptor *rfa;
  Slice *slice;
  Vector *features;
  int i;
  int failed;
  
  initEnsC(argc, argv);

  dba = Test_initROEnsDB();

  slice = Test_getStandardSlice(dba);

  ok(1, slice!=NULL);

  rfa = DBAdaptor_getRepeatFeatureAdaptor(dba);

  ok(2, rfa!=NULL);

  features =  Slice_getAllRepeatFeatures(slice,NULL,NULL, NULL);

  ok(3, features!=NULL);
  ok(4, Vector_getNumElement(features)!=0);

  failed = 0;
  for (i=0;i<Vector_getNumElement(features) && !failed;i++) {
    RepeatFeature *rf = Vector_getElementAt(features,i);
    int start = RepeatFeature_getStart(rf);
    int end   = RepeatFeature_getEnd(rf);
    Vector *rrfVector;
    RepeatFeature *rrf;

    printf("slice start = %d end = %d\n",start,end);
/*
    rrfVector = RepeatFeature_transformToRawContig(rf);
    if (Vector_getNumElement(rrfVector) > 1) {
      printf("Feature mapped to more than one rawcontig\n");
      failed=1;
    }
    rrf = Vector_getElementAt(rrfVector,0);

    //printf("rc start = %d end = %d\n",RepeatFeature_getStart(rrf),RepeatFeature_getEnd(rrf));
    rf = RepeatFeature_transformToSlice(rrf, slice);
    if (RepeatFeature_getStart(rf) != start ||
        RepeatFeature_getEnd(rf) != end) {
      printf("Remapping to slice produced different coords\n");
      failed =1;
    }
*/
  }
  ok(5, !failed);
  return 0;
}

Exemplo n.º 2

int main(int argc, char *argv[]) {
  DBAdaptor *dba;
  DBAdaptor *writeDba;
  ProteinAlignFeatureAdaptor *pafa;
  Slice *slice;
  Vector *features;
  int i;
  int failed;
  
  initEnsC(argc, argv);

  dba = Test_initROEnsDB();

  writeDba = Test_initRWEnsDB();

  slice = Test_getStandardSlice(dba);

  ok(1, slice!=NULL);

  pafa = DBAdaptor_getProteinAlignFeatureAdaptor(writeDba);
  SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(dba);

  ok(2, pafa!=NULL);

  //features =  Slice_getAllDNAPepAlignFeatures(slice,NULL,NULL, NULL,NULL);

  //Slice *slice3 = SliceAdaptor_fetchByRegion(sa,"chromosome","1",2,260000000,1,NULL,0);
  Slice *slice2 = SliceAdaptor_fetchByRegion(sa,"chromosome","1",1000000,4000000,1,NULL,0);
  features =  Slice_getAllProteinAlignFeatures(slice2,NULL,NULL, NULL,NULL);

  ok(3, features!=NULL);
  ok(4, Vector_getNumElement(features)!=0);

  ProteinAlignFeatureAdaptor_store((BaseFeatureAdaptor*)pafa, features);

  return 0;
}

Exemplo n.º 3

int main(int argc, char *argv[]) {
  DBAdaptor *dba;
  GeneAdaptor *ga;
  Slice *slice = NULL;
  Vector *genes = NULL;
  int i = 0;
  int failed = 0;
  
  initEnsC(argc, argv);

//  ProcUtil_showBacktrace(EnsC_progName);

  dba = Test_initROEnsDB();
  slice = Test_getStandardSlice(dba);

//  DBAdaptor *seqdba = DBAdaptor_new("genebuild6.internal.sanger.ac.uk","ensadmin","ensembl","steve_chicken_rnaseq_missing_reference",3306,NULL);
//  dba = DBAdaptor_new("genebuild1.internal.sanger.ac.uk","ensadmin","ensembl","steve_chicken_rnaseq_missing_refined",3306,seqdba);

  ok(1, slice!=NULL);

  ga = DBAdaptor_getGeneAdaptor(dba);
  SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(dba);

  ok(2, ga!=NULL);

  slice = SliceAdaptor_fetchByRegion(sa,"chromosome","20",10000000,50000000,1,NULL,0);
//  slice = SliceAdaptor_fetchByRegion(sa,"chromosome","17",1000000,5000000,1,NULL,0);
//  slice = SliceAdaptor_fetchByRegion(sa,"chromosome","17",1,5000000,1,NULL,0);
// Has a seleno
//  slice = SliceAdaptor_fetchByRegion(sa,"chromosome","1",1000000,27000000,1,NULL,0);
//  slice = SliceAdaptor_fetchByRegion(sa,"chromosome","MT",1,17000,1,NULL,0);
  genes =  Slice_getAllGenes(slice, NULL, NULL, 1, NULL, NULL);

  fprintf(stdout, "Have %d genes\n", Vector_getNumElement(genes));
  ok(3, genes!=NULL);
  ok(4, Vector_getNumElement(genes)!=0);

  failed = dumpGenes(genes, 1);
  ok(5, !failed);

  //Vector *toplevelSlices = SliceAdaptor_fetchAll(sa, "toplevel", NULL, 0);
  Vector *toplevelSlices = SliceAdaptor_fetchAll(sa, "chromosome", NULL, 0);

  for (i=0;i<Vector_getNumElement(toplevelSlices) && !failed;i++) {
    Slice *tlSlice = Vector_getElementAt(toplevelSlices, i);
    fprintf(stderr, "Slice %s\n", Slice_getName(tlSlice));
    genes =  Slice_getAllGenes(tlSlice, NULL, NULL, 1, NULL, NULL);
    fprintf(stderr, "Got %d genes on %s\n", Vector_getNumElement(genes), Slice_getName(tlSlice));
    failed = dumpGenes(genes, 0);
  }

  //tc_malloc_stats();

  fprintf(stderr,"\nEcostring table stats:\n");
  EcoString_getInfo(ecoSTable);

  fprintf(stderr,"\n");
  ProcUtil_timeInfo("at end of GeneTest");

  return 0;
}