Genomic * get_Genomic_from_Gene(Gene * gene)
{
Genomic * gn;
char buffer[64];
/* fprintf(stdout,"Getting genomic...\n"); */
if( gene->genomic != NULL )
return gene->genomic;
if( gene->parent == NULL ) {
warn("Cannot get Gene, as no parent genomic region!");
return NULL;
}
gn = get_Genomic_from_GenomicRegion(gene->parent);
if( gn == NULL) {
warn("Cannot get Gene, as no sequence in genomic region!");
return NULL;
}
if( gn->baseseq->offset < gn->baseseq->end) {
if( gene->start > gene->end )
gene->genomic = truncate_Genomic(gn,gene->start-gn->baseseq->offset+2,gene->end-gn->baseseq->offset+2);
else
gene->genomic = truncate_Genomic(gn,gene->start-gn->baseseq->offset+1,gene->end-gn->baseseq->offset+1);
}
else {
gene->genomic = truncate_Genomic(gn,gn->baseseq->offset-1 - gene->start,gn->baseseq->offset-1 - gene->end);
}
sprintf(buffer,"%s.[%d:%d]",Genomic_name(gn),gene->start+1,gene->end);
ckfree(gene->genomic->baseseq->name);
gene->genomic->baseseq->name = stringalloc(buffer);
return gene->genomic;
}
cDNA * get_cDNA_from_Transcript(Transcript * trs)
{
Genomic * gn;
Sequence * base;
int i;
char buffer[64];
if( trs->cDNA != NULL)
return trs->cDNA;
if( trs->parent == NULL ) {
warn("Cannot get cDNA, as no parent Gene!");
return NULL;
}
if ( (gn = get_Genomic_from_Gene(trs->parent)) == NULL ) {
warn("Cannot get cDNA, as cannot get Genomic sequence from Gene");
return NULL;
}
base = Sequence_alloc();
sprintf(buffer,"%s.sp",Genomic_name(gn));
base->name = stringalloc(buffer);
base->seq = ckcalloc(length_Transcript(trs)+1,sizeof(char));
base->seq[0]='\0';
for(i=0;i<trs->ex_len;i++) {
strncat(base->seq,gn->baseseq->seq+trs->exon[i]->start,trs->exon[i]->end-trs->exon[i]->start);
}
make_len_type_Sequence(base);
base->type = SEQUENCE_CDNA;
trs->cDNA = cDNA_from_Sequence(base);
return trs->cDNA;
}
