C++ (Cpp) cDNA_from_Sequence Examples

Example #1

File: cdnadb.c Project: PlantandFoodResearch/wise2

cDNA * get_cDNA_from_cDNADB(cDNADB * cdnadb,DataEntry * de)
{
  Sequence * seq;
  Sequence * temp;

  if( cdnadb == NULL ) {
    warn("Cannot get entry from a null database");
    return NULL;
  }

  if( de == NULL ) {
    warn("Cannot get entry with a null dataentry");
    return NULL;
  }


  if( cdnadb->is_single_seq == TRUE ) {
    if( de->is_reversed == TRUE ) 
      return cDNA_from_Sequence(hard_link_Sequence(cdnadb->rev->seq));
    else 
      return cDNA_from_Sequence(hard_link_Sequence(cdnadb->forw->seq));
  }

  /* we need to get out the Sequence from seqdb */

  seq = get_Sequence_from_SequenceDB(cdnadb->sdb,de);
  if( seq == NULL ) {
    warn("Cannot get entry for %s from cDNA db",de->name);
    return NULL;
  }

  if( seq->type != SEQUENCE_DNA) {
    warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
  }

  force_to_dna_Sequence(seq,1.0,NULL);

  if( de->is_reversed == TRUE ) {
    temp = reverse_complement_Sequence(seq);
    free_Sequence(seq);
    seq = temp;
  }

  return cDNA_from_Sequence(seq);
}

Example #2

File: transcript.c Project: mrmckain/RefTrans

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;
}