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;
}
char *PredictionExon_getSeqString(PredictionExon *exon) {
char *seq;
if (PredictionExon_getSeqCacheString(exon)) {
return PredictionExon_getSeqCacheString(exon);
}
if (!PredictionExon_getSlice(exon)) {
fprintf(stderr, "Warning: this exon %s doesn't have a contig you won't get a seq\n", PredictionExon_getDisplayLabel(exon));
return NULL;
} else {
seq = BaseContig_getSubSeq(PredictionExon_getSlice(exon),
PredictionExon_getStart(exon),
PredictionExon_getEnd(exon),
1);
if (PredictionExon_getStrand(exon) == -1){
SeqUtil_reverseComplement(seq,strlen(seq));
}
}
PredictionExon_setSeqCacheString(exon, seq);
return PredictionExon_getSeqCacheString(exon);
}
void compareComplements(Slice *slice, SequenceAdaptor *seqA) {
char *seq = SequenceAdaptor_fetchBySliceStartEndStrand(seqA, slice,1,POS_UNDEF,1);
fprintf(stderr,"FORWARD STRAND SLICE SEQ for %s\n", Slice_getName(slice));
//fprintf(stderr,"%s\n", seq);
char *invertedSeq = SequenceAdaptor_fetchBySliceStartEndStrand(seqA, slice,1,POS_UNDEF,-1);
fprintf(stderr,"REVERSE STRAND SLICE SEQ for %s\n", Slice_getName(slice));
//fprintf(stderr,"%s\n", invertedSeq);
ok(nTest++, strlen(seq) == Slice_getLength(slice)); //sequence is correct length
SeqUtil_reverseComplement(seq, Slice_getLength(slice)); //reverse complement seq
//fprintf(stderr,"%s\n", seq);
ok(nTest++, !strcmp(seq, invertedSeq)); //revcom same as seq on inverted slice
}
