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; 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; }