Retain Capitalization For Features

Question

[Lee Katz]

Hi, I have a GenBank file and am extracting a gene upstream and downstream of a target gene, with everything in between (3 genes + 2 intergenic regions). I am loading the sequence in BioPerl and outputting the sequence to a file.

However, I want to make genes uppercase and intergenic regions lowercase. Is there an easy way to do this? Is there a clean BioPerl way?

sub extractSeq{
  my($file,$start,$end,$settings)=@_;
  my $targetSeq;
  my $seqin=Bio::SeqIO->new(-file=>$file);
  if($$settings{contig}){
    while(my $seq=$seqin->next_seq){
      if($seq->id eq $$settings{contig}){
        $targetSeq=$seq;
        last;
      }
    }
  } else {
    $targetSeq=$seqin->next_seq;
  }

  my $sequence=$targetSeq->subseq($start,$end);

  my $genomeName=basename($file,qw(.gbk .gbk.fna));
  my $extractedSeq=Bio::Seq->new(-id=>join("_",$genomeName,$$settings{contig},$start,$end),-seq=>$sequence);
  $extractedSeq=$extractedSeq->revcom if($$settings{revcom});
  return $extractedSeq;
}

Answer 1

[Lee Katz]

sub highlightFeatures{ my($seq,$settings)=@_; my $highlight=$$settings{highlight_type}||"uc"; # TODO return false if not a rich seq for my $feat($seq->get_SeqFeatures){ next if($feat->primary_tag eq 'source'); my($start,$end)=($feat->location->start,$feat->location->end); if($highlight eq 'uc'){ my $firstPartOfTheSequence=($start>1)?$seq->subseq(1,$start-1):""; my $lastPartOfTheSequence=($end<$seq->length)?$seq->subseq($end+1,$seq->length):""; my $sequence=$firstPartOfTheSequence.uc($seq->subseq($start,$end)).$lastPartOfTheSequence; $seq->seq($sequence); } } }