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;
}
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;
}
int main(int argc, char *argv[]) {
DBAdaptor *dba;
AssemblyMapperAdaptor *asma;
int testNum = 1;
initEnsC(argc, argv);
dba = Test_initROEnsDB();
//
// 1 Test AssemblyMapperAdaptor constructor
//
asma = DBAdaptor_getAssemblyMapperAdaptor(dba);
ok(testNum++, asma!=NULL);
//
// Test fetch_by_CoordSystems
//
CoordSystemAdaptor *csa = DBAdaptor_getCoordSystemAdaptor(dba);
CoordSystemAdaptor_dumpCachedMappings(csa);
CoordSystem *toplevelCs = CoordSystemAdaptor_fetchByName(csa, "toplevel", NULL);
CoordSystem *clnCs = CoordSystemAdaptor_fetchByName(csa, "clone", NULL);
CoordSystem *superctgCs = CoordSystemAdaptor_fetchByName(csa, "supercontig", NULL);
TopLevelAssemblyMapper *clnToplevelMapper = (TopLevelAssemblyMapper *)AssemblyMapperAdaptor_fetchByCoordSystems(asma, toplevelCs, clnCs);
TopLevelAssemblyMapper *superctgToplevelMapper = (TopLevelAssemblyMapper *)AssemblyMapperAdaptor_fetchByCoordSystems(asma, toplevelCs, superctgCs);
ok(testNum++, clnToplevelMapper!=NULL); // && $cln_toplevel_mapper->isa('Bio::EnsEMBL::TopLevelAssemblyMapper'));
ok(testNum++, superctgToplevelMapper!=NULL); // && $cln_toplevel_mapper->isa('Bio::EnsEMBL::TopLevelAssemblyMapper'));
//
// test db has chr 20 (50KB -> 62MB)
//
//
// Test map
//
MapperRangeSet *coords = NULL;
if (clnToplevelMapper) {
fprintf(stderr, "MAP 'AL359765.6'->toplevel\n");
coords = TopLevelAssemblyMapper_map(clnToplevelMapper,"AL359765.6", 1, 13780, 1, clnCs, 0, NULL);
printCoords(coords);
ok(testNum++, coords!=NULL);
}
if (superctgToplevelMapper) {
fprintf(stderr, "MAP NT_028392->toplevel\n");
coords = TopLevelAssemblyMapper_map(superctgToplevelMapper, "NT_028392", 600000, 1000000, 1, superctgCs, 0, NULL);
printCoords(coords);
ok(testNum++, coords!=NULL);
}
//
// Test list_seq_regions
//
Vector *seqRegions;
int i;
if (clnToplevelMapper) {
seqRegions = TopLevelAssemblyMapper_listSeqRegions(clnToplevelMapper, "AL359765.6", 1, 13780, clnCs);
ok(testNum++, seqRegions!=NULL && Vector_getNumElement(seqRegions) == 1 && !strcmp("20", Vector_getElementAt(seqRegions,0)));
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
if (superctgToplevelMapper) {
seqRegions = TopLevelAssemblyMapper_listSeqRegions(superctgToplevelMapper, "NT_028392", 600000, 1000000, superctgCs);
ok(testNum++, seqRegions!=NULL && Vector_getNumElement(seqRegions) == 1 && !strcmp("20", Vector_getElementAt(seqRegions,0)));
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
//
// Test list_seq_ids
//
Vector *ids;
if (clnToplevelMapper) {
ids = TopLevelAssemblyMapper_listIds(clnToplevelMapper, "AL359765.6", 1, 13780, clnCs);
ok(testNum++, ids!=NULL && Vector_getNumElement(ids) == 1 && *((IDType *)Vector_getElementAt(ids,0)) == 469283 );
for (i=0;i<Vector_getNumElement(ids); i++) {
IDType id = *((IDType *)Vector_getElementAt(ids, i));
fprintf(stderr, IDFMTSTR"\n",id);
}
}
if (superctgToplevelMapper) {
ids = TopLevelAssemblyMapper_listIds(superctgToplevelMapper, "NT_028392", 600000, 1000000, superctgCs);
ok(testNum++, ids!=NULL && Vector_getNumElement(ids) == 1 && *((IDType *)Vector_getElementAt(ids,0)) == 469283 );
for (i=0;i<Vector_getNumElement(ids); i++) {
IDType id = *((IDType *)Vector_getElementAt(ids, i));
fprintf(stderr, IDFMTSTR"\n",id);
}
}
// Test for a not implemented method
// seqRegions = TopLevelAssemblyMapper_listContigIds(clnToplevelMapper, "AL359765.6", 1, 13780, 1);
return 0;
}
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;
}
int main(int argc, char *argv[]) {
DBAdaptor *dba;
AssemblyMapperAdaptor *asma;
int testNum = 1;
initEnsC(argc, argv);
dba = Test_initROEnsDB();
//
// 1 Test AssemblyMapperAdaptor constructor
//
asma = DBAdaptor_getAssemblyMapperAdaptor(dba);
ok(testNum++, asma!=NULL);
//
// 2 Test fetch_by_CoordSystems
//
CoordSystemAdaptor *csa = DBAdaptor_getCoordSystemAdaptor(dba);
CoordSystemAdaptor_dumpCachedMappings(csa);
CoordSystem *chrCs = CoordSystemAdaptor_fetchByName(csa, "chromosome", NULL);
CoordSystem *clnCs = CoordSystemAdaptor_fetchByName(csa, "clone", NULL);
CoordSystem *sCtgCs = CoordSystemAdaptor_fetchByName(csa, "supercontig", NULL);
ChainedAssemblyMapper *asmMapper = (ChainedAssemblyMapper *)AssemblyMapperAdaptor_fetchByCoordSystems(asma, clnCs, chrCs);
ok(testNum++, asmMapper!=NULL); // Need to make it an object before can do this && asmMapper->objectType == ( "Bio::EnsEMBL::ChainedAssemblyMapper" ));
ChainedAssemblyMapper *chrSCtgMapper = (ChainedAssemblyMapper *)AssemblyMapperAdaptor_fetchByCoordSystems(asma, chrCs, sCtgCs);
ok(testNum++, chrSCtgMapper!=NULL);// && $chr_sctg_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper'));
//
// test db has chr 20 (50KB -> 62MB)
//
MapperRangeSet *coords;
if (asmMapper)
{
fprintf(stderr,"MAP 20->clone\n");
coords = ChainedAssemblyMapper_map(asmMapper, "20", 500001, 60000000, 1, chrCs, 0, NULL);
ok(testNum++, coords!=NULL);
printCoords(coords);
}
if (asmMapper)
{
fprintf(stderr,"MAP 'AL359765.6'->chromosome\n");
coords = ChainedAssemblyMapper_map(asmMapper, "AL359765.6", 1, 13780, 1, clnCs, 0, NULL);
ok(testNum++, coords!=NULL);
printCoords(coords);
}
if (chrSCtgMapper)
{
fprintf(stderr,"MAP 20->supercontig\n");
coords = ChainedAssemblyMapper_map(chrSCtgMapper, "20", 500001, 60000000, 1, chrCs, 0, NULL);
ok(testNum++, coords!=NULL);
printCoords(coords);
}
//
// Test list_seq_regions
//
fprintf(stderr,"Starting list tests\n");
int i;
if (asmMapper)
{
Vector *seqRegions = ChainedAssemblyMapper_listSeqRegions(asmMapper, "20", 500001, 60000000, chrCs);
ok(testNum++, seqRegions != NULL);
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
if (asmMapper)
{
Vector *seqRegions = ChainedAssemblyMapper_listSeqRegions(asmMapper, "AL359765.6", 1, 13780, clnCs);
ok(testNum++, seqRegions!=NULL);
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
if (chrSCtgMapper)
{
Vector *seqRegions = ChainedAssemblyMapper_listSeqRegions(chrSCtgMapper, "NT_028392", 600000, 1000000, sCtgCs);
ok(testNum++, seqRegions!=NULL);
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
if (chrSCtgMapper)
{
Vector *seqRegions = ChainedAssemblyMapper_listSeqRegions(chrSCtgMapper, "20", 3000000, 31000000, chrCs);
ok(testNum++, seqRegions!=NULL);
for (i=0;i<Vector_getNumElement(seqRegions); i++) {
char *regionName = Vector_getElementAt(seqRegions, i);
fprintf(stderr, "%s\n",regionName);
}
}
//
// Test list_seq_ids
//
if (asmMapper)
{
Vector *seqIds = ChainedAssemblyMapper_listIds(asmMapper, "20", 500001, 60000000, chrCs);
ok(testNum++, seqIds!=NULL);
for (i=0;i<Vector_getNumElement(seqIds); i++) {
IDType regionId = *((IDType *)Vector_getElementAt(seqIds, i));
fprintf(stderr, IDFMTSTR"\n",regionId);
}
}
if (asmMapper)
{
Vector *seqIds = ChainedAssemblyMapper_listIds(asmMapper, "AL359765.6", 1, 13780, clnCs);
ok(testNum++, seqIds!=NULL);
for (i=0;i<Vector_getNumElement(seqIds); i++) {
IDType regionId = *((IDType *)Vector_getElementAt(seqIds, i));
fprintf(stderr, IDFMTSTR"\n",regionId);
}
}
if (chrSCtgMapper)
{
Vector *seqIds = ChainedAssemblyMapper_listIds(chrSCtgMapper, "NT_028392", 600000, 1000000, sCtgCs);
ok(testNum++, seqIds!=NULL);
for (i=0;i<Vector_getNumElement(seqIds); i++) {
IDType regionId = *((IDType *)Vector_getElementAt(seqIds, i));
fprintf(stderr, IDFMTSTR"\n",regionId);
}
}
if (chrSCtgMapper)
{
Vector *seqIds = ChainedAssemblyMapper_listIds(chrSCtgMapper, "20", 3000000, 31000000, chrCs);
ok(testNum++, seqIds!=NULL);
for (i=0;i<Vector_getNumElement(seqIds); i++) {
IDType regionId = *((IDType *)Vector_getElementAt(seqIds, i));
fprintf(stderr, IDFMTSTR"\n",regionId);
}
}
return 0;
}
