int main(int argc, char *argv[]) {
DBAdaptor *dba;
Slice *slice;
SliceAdaptor *sliceA;
SequenceAdaptor *seqA;
initEnsC(argc, argv);
dba = DBAdaptor_new("ensembldb.ensembl.org","anonymous",NULL,"homo_sapiens_core_70_37",5306,NULL);
//dba = DBAdaptor_new("ens-livemirror.internal.sanger.ac.uk","ensro",NULL,"homo_sapiens_core_70_37",3306,NULL);
//dba = DBAdaptor_new("genebuild2.internal.sanger.ac.uk","ensadmin","ensembl","steve_hs_testdb",3306,NULL);
sliceA = DBAdaptor_getSliceAdaptor(dba);
seqA = DBAdaptor_getSequenceAdaptor(dba);
//
// Test fetch_by_Slice_start_end_strand
//
slice = SliceAdaptor_fetchByRegion(sliceA,"chromosome",CHR,START,END,STRAND,NULL,0);
compareComplements(slice, seqA);
slice = SliceAdaptor_fetchByRegion(sliceA, "clone","AL031658.11", POS_UNDEF, POS_UNDEF, STRAND_UNDEF, NULL, 0);
compareComplements(slice, seqA);
slice = SliceAdaptor_fetchByRegion(sliceA, "supercontig","NT_028392", POS_UNDEF, POS_UNDEF, STRAND_UNDEF, NULL, 0);
compareComplements(slice, seqA);
slice = SliceAdaptor_fetchByRegion(sliceA, "contig", "AL031658.11.1.162976", POS_UNDEF, POS_UNDEF, STRAND_UNDEF, NULL, 0);
compareComplements(slice, seqA);
return 0;
}
int main(int argc, char *argv[]) {
Vector *pieces;
char *str;
char *reverse;
int testResult = 0;
initEnsC(argc, argv);
pieces = CigarStrUtil_getPieces(cigar1);
testResult += ok(1, Vector_getNumElement(pieces) == 6);
str = Vector_getElementAt(pieces,0);
testResult += ok(2, !strcmp(str,"6M"));
Vector_free(pieces);
StrUtil_copyString(&str,cigar1,0);
testResult += ok(3, !strcmp(str,cigar1));
reverse = CigarStrUtil_reverse(str,strlen(str));
free(str);
pieces = CigarStrUtil_getPieces(reverse);
testResult += ok(4, Vector_getNumElement(pieces) == 6);
str = Vector_getElementAt(pieces,0);
testResult += ok(5, !strcmp(str,"M"));
return testResult;
}
int main(int argc, char *argv[]) {
ComparaDBAdaptor *cdba;
initEnsC(argc, argv);
cdba = ComparaDBAdaptor_new("kaka.sanger.ac.uk","anonymous",NULL,"ensembl_compara_14_1",3306,"Tests/Compara.conf");
return 0;
}
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[]) {
initEnsC(argc, argv);
Mapper *mapper = Mapper_new( "rawcontig", "virtualcontig", NULL, NULL );
int nToLoad = loadSGPDump(mapper, 0 );
// loading done successfully
ok(1, nToLoad == 100);
{
// transform a segment entirely within the first rawcontig
int testOutput[][4] = {1, 2, 5, -1};
testTransform (mapper, 627012, 2, 5, -1, "rawcontig", testOutput, NumOutput(testOutput));
}
{
// now a split coord
int testOutput[][4] = {
{314696, 31917, 31937, -1},
{341, 126, 59773, -1},
{315843, 5332, 5963, +1}
};
testTransform (mapper, 1, 383700, 444000, +1, "virtualcontig",testOutput, NumOutput(testOutput));
}
{
// now a simple gap
int testOutput[][4] = {
{ 627011, 7447, 7507, +1 },
{ 1, 273762, 273781, 0 }
};
testTransform (mapper, 1, 273701, 273781, +1, "virtualcontig", testOutput, NumOutput(testOutput));
}
//
// check if the mapper can do merging
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, 1, 1, 111, 120 );
{
int testOutput[][4] = {{ 1, 105, 125, 1 }};
testTransform(mapper, 1, 5, 25, 1, "asm1", testOutput, NumOutput(testOutput));
}
//
// Slightly differnt merge case
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 12, 20, 1, 1, 112, 120 );
{
int testOutput[][4] = {
{ 1, 105, 110, 1 },
{ 1, 11, 11, 0 },
{ 1, 112, 125, 1 }
};
testTransform( mapper, 1, 5, 25, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// dont merge on wrong orientation
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, 1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, -1, 1, 111, 120 );
{
int testOutput[][4] = {
{ 1, 105, 110, 1 },
{ 1, 111, 120, -1 },
{ 1, 121, 125, 1 }
};
testTransform( mapper, 1, 5, 25, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// can reverse strands merge?
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, -1, 1, 121, 130 );
Mapper_addMapCoordinates(mapper, 1, 21, 30, -1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, -1, 1, 111, 120 );
{
int testOutput[][4] = {{ 1, 106, 126, -1 } };
testTransform( mapper, 1, 5, 25, 1, "asm1", testOutput, NumOutput(testOutput));
}
//
// normal merge, not three
//
mapper = Mapper_new( "asm1", "asm2", NULL, NULL );
Mapper_addMapCoordinates(mapper, 1, 1, 10, 1, 1, 101, 110 );
Mapper_addMapCoordinates(mapper, 1, 11, 20, 1, 1, 111, 120 );
Mapper_addMapCoordinates(mapper, 1, 22, 30, 1, 1, 132, 140 );
Mapper_addMapCoordinates(mapper, 1, 51, 70, 1, 1, 161, 180 );
Mapper_addMapCoordinates(mapper, 1, 31, 35, 1, 1, 141, 145 );
{
int testOutput[][4] = {
{ 1, 105, 120, 1 },
{ 1, 21, 21, 0 },
{ 1, 132, 145, 1 },
{ 1, 36, 45, 0 }
};
testTransform( mapper, 1, 5, 45, 1, "asm1" , testOutput, NumOutput(testOutput));
}
//
// test tranformation of 'insertion' coordinates where end = start -1
//
mapper = Mapper_new("asm1", "asm2", NULL, NULL);
Mapper_addMapCoordinates(mapper,1, 1, 10, 1, 2, 101, 110);
Mapper_addMapCoordinates(mapper,1, 11, 20, -1, 3, 1, 10);
{
// boundary insert, expect 2 edge inserts back
int testOutput[][4] = {
{2, 111, 110, 1},
{3, 11, 10, -1}
};
testTransform(mapper, 1, 11, 10, 1, "asm1", testOutput, NumOutput(testOutput));
}
{
// edge insert, negative strand, expect edge insert negative strand
int testOutput[][4] = {{2, 101, 100, -1}};
testTransform(mapper, 1, 1, 0, -1, "asm1", testOutput, NumOutput(testOutput));
}
{
// normal case, expect single insert in middle
int testOutput[][4] = {{2, 102, 101, 1}};
testTransform(mapper, 1, 2, 1, 1, "asm1", testOutput, NumOutput(testOutput));
}
{
// expect a gap
int testOutput[][4] = {{1, 100, 200, 0}};
testTransform(mapper, 1, 100, 200, 1, "asm1", testOutput, NumOutput(testOutput));
}
return 0;
}
int main(int argc, char *argv[]) {
DBAdaptor * dba;
StatementHandle *sth;
ResultRow * row;
Vector * slices;
int nSlices;
htsFile * out;
int argNum = 1;
char *inFName = NULL;
char *outFName = NULL;
char *dbUser = "******";
char *dbPass = NULL;
int dbPort = 3306;
char *dbHost = "ens-staging.internal.sanger.ac.uk";
char *dbName = "homo_sapiens_core_71_37";
char *assName = "GRCh37";
char *chrName = "1";
int flags = 0;
int threads = 1;
initEnsC(argc, argv);
while (argNum < argc) {
char *arg = argv[argNum];
char *val;
// Ones without a val go here
if (!strcmp(arg, "-U") || !strcmp(arg,"--ucsc_naming")) {
flags |= M_UCSC_NAMING;
} else {
// Ones with a val go in this block
if (argNum == argc-1) {
Bamcov_usage();
}
val = argv[++argNum];
if (!strcmp(arg, "-i") || !strcmp(arg,"--in_file")) {
StrUtil_copyString(&inFName,val,0);
} else if (!strcmp(arg, "-o") || !strcmp(arg,"--out_file")) {
StrUtil_copyString(&outFName,val,0);
} else if (!strcmp(arg, "-h") || !strcmp(arg,"--host")) {
StrUtil_copyString(&dbHost,val,0);
} else if (!strcmp(arg, "-p") || !strcmp(arg,"--password")) {
StrUtil_copyString(&dbPass,val,0);
} else if (!strcmp(arg, "-P") || !strcmp(arg,"--port")) {
dbPort = atoi(val);
} else if (!strcmp(arg, "-n") || !strcmp(arg,"--name")) {
StrUtil_copyString(&dbName,val,0);
} else if (!strcmp(arg, "-u") || !strcmp(arg,"--user")) {
StrUtil_copyString(&dbUser,val,0);
} else if (!strcmp(arg, "-t") || !strcmp(arg,"--threads")) {
threads = atoi(val);
} else if (!strcmp(arg, "-a") || !strcmp(arg,"--assembly")) {
StrUtil_copyString(&assName,val,0);
} else if (!strcmp(arg, "-v") || !strcmp(arg,"--verbosity")) {
verbosity = atoi(val);
// Temporary
} else if (!strcmp(arg, "-c") || !strcmp(arg,"--chromosome")) {
StrUtil_copyString(&chrName,val,0);
} else {
fprintf(stderr,"Error in command line at %s\n\n",arg);
Bamcov_usage();
}
}
argNum++;
}
if (verbosity > 0) {
printf("Program for calculating read coverage in a BAM file \n"
"Steve M.J. Searle. [email protected] Last update April 2013.\n");
}
if (!inFName || !outFName) {
Bamcov_usage();
}
dba = DBAdaptor_new(dbHost,dbUser,dbPass,dbName,dbPort,NULL);
//nSlices = getSlices(dba, destName);
nSlices = 1;
slices = Vector_new();
SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(dba);
Slice *slice = SliceAdaptor_fetchByRegion(sa,NULL,chrName,POS_UNDEF,POS_UNDEF,1,NULL, 0);
Vector_addElement(slices,slice);
if (Vector_getNumElement(slices) == 0) {
fprintf(stderr, "Error: No slices.\n");
exit(1);
}
htsFile *in = hts_open(inFName, "rb");
if (in == 0) {
fprintf(stderr, "Fail to open BAM file %s\n", inFName);
return 1;
}
hts_set_threads(in, threads);
hts_idx_t *idx;
idx = bam_index_load(inFName); // load BAM index
if (idx == 0) {
fprintf(stderr, "BAM index file is not available.\n");
return 1;
}
int i;
for (i=0; i<Vector_getNumElement(slices); i++) {
Slice *slice = Vector_getElementAt(slices,i);
if (verbosity > 0) printf("Working on '%s'\n",Slice_getName(slice));
// if (verbosity > 0) printf("Stage 1 - retrieving annotation from database\n");
// Vector *genes = getGenes(slice, flags);
if (verbosity > 0) printf("Stage 1 - calculating coverage\n");
calcCoverage(inFName, slice, in, idx, flags);
}
hts_idx_destroy(idx);
hts_close(in);
if (verbosity > 0) printf("Done\n");
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;
}
