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;
}
Protein * get_Protein_from_Translation(Translation * ts,CodonTable * ct)
{
cDNA * cd;
int i,j;
Sequence * seq;
char buffer[64];
assert(ts);
assert(ct);
/* fprintf(stderr,"Codon table is %d\n",ct);*/
if( ts->protein != NULL)
return ts->protein;
if( ts->parent == NULL ) {
warn("Cannot get Protein from translation as no parent!");
return NULL;
}
cd = get_cDNA_from_Transcript(ts->parent);
if( cd == NULL ) {
warn("Cannot make translation as can't get transcript!");
return NULL;
}
if( cd->baseseq == NULL ) {
warn("A bad error - a non NULL cDNA with a null sequence object. No translation here!");
return NULL;
}
if( cd->baseseq->len == 0 ) {
warn("Attempting to translate a zero length cDNA. Yikes!");
return NULL;
}
seq = Sequence_alloc();
sprintf(buffer,"%s.tr",cDNA_name(cd));
seq->name = stringalloc(buffer);
seq->seq = ckcalloc((cd->baseseq->len/3) + 2,sizeof(char));
seq->type = SEQUENCE_PROTEIN;
if( cd->baseseq->len%3 != 0 ) {
warn("Problem in making translation, cDNA is not mod3! - length is %d - transcript id %s",cd->baseseq->len,seq->name);
}
for(i=0,j=0;i<cd->baseseq->len;i+=3,j++) {
if( is_stop_codon(codon_from_seq(cd->baseseq->seq+i),ct) == TRUE ) {
if( i+3 >= cd->baseseq->len )
break;
else {
warn("Got a stop codon in the middle of a translation at postion [%d]. Yuk!",i);
seq->seq[j] = '*';
}
} else {
seq->seq[j] = aminoacid_from_seq(ct,cd->baseseq->seq+i);
}
}
seq->seq[j]='\0';
make_len_type_Sequence(seq);
/*write_fasta_Sequence(seq,stdout);*/
seq->type = SEQUENCE_PROTEIN;
ts->protein = Protein_from_Sequence(seq);
return ts->protein;
}
