char *RawContig_getSubSeq(RawContig *contig, int start, int end, int strand) {
SequenceAdaptor *sa;
if (end < start) {
fprintf(stderr, "Error: End coord is less then start coord to call on RawContig subseq.");
exit(1);
}
if (strand != -1 && strand != 1) {
strand = 1;
}
// if the sequence of this contig has been manually set retrieve its substring
if (contig->seq) {
char *str = StrUtil_substr(contig->seq, start-1, end - start + 1);
if (strand == -1) {
SeqUtil_reverseComplement(str,strlen(str));
}
return str;
}
if (!RawContig_getAdaptor(contig)) {
fprintf(stderr, "Error: RawContig subseq no sequence set and no db available\n");
return emptyString;
}
sa = DBAdaptor_getSequenceAdaptor(RawContig_getAdaptor(contig)->dba->dnadb);
//return SequenceAdaptor_fetchByRawContigStartEndStrand(sa, RawContig_getDbID(contig), start, end, strand);
return NULL;
}
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;
}
char *RawContig_getSeq(RawContig *contig) {
if (contig->seq) {
return contig->seq;
}
//or retrieved from the database
if (RawContig_getAdaptor(contig)) {
DBAdaptor *dnadba;
SequenceAdaptor *sa;
dnadba = RawContig_getAdaptor(contig)->dba->dnadb;
sa = DBAdaptor_getSequenceAdaptor(dnadba);
//return SequenceAdaptor_fetchByRawContigStartEndStrand(sa, RawContig_getDbID(contig), 1, -1, 1);
return NULL;
}
fprintf(stderr,"Warning: RawContig seq not set, and no db is available\n");
return emptyString;
}