[Bioperl-l] sequence upgrading

[Heikki Lehvaslaiho]

Marc,

I think Hilmar suggests adding something like this into 
Bio::Seq::RichSeq:


sub copy {
    my ($self, $seq) = @_;
    unless (defined $seq) {
        # return a deep copy of $self
        my $newseq = new $self;
        # ... copy attributes

        return $newseq;
    }
    if ($seq->isa('Bio::PrimarySeqI') ) {
        my $newseq = new $self;
        @primaryseqmethods = qw( seq display_id ...);
        map {$newseq->$_($seq->$_) } @primaryseqmethods;
        return $newseq if $seq->isa('Bio::PrimarySeq');

        # either deal with all other methods by class
        @seqmethods = qw( species ...);

        # or test them all one by one
        $newseq->species($seq->species) if $seq->can('spacies');
        # ...
        returnt $newseq;
    } else {
     $self->throw("Can copy only sequence objects, not ". ref $seq.
"\n");
    }

}

Actually, the whole problem of dealing with attributes is solved in a
CPAN module Clone which does deep copying of structures.

With it you can simply say:

use Clone qw(clone);
# $seq can be e.g. Bio::Seq with features
my $seq2 = clone $seq;

However, simply 'use'ing Clone in sequence classes would add an external
dependency into bioperl core classes, which is not acceptable.  I am
sure there are many clever solutions to this problem, though.

	-Heikki

On Thu, 2003-06-26 at 10:43, Marc Logghe wrote:
> > 
> > This depends entirely on your implementation. E.g., if you put a copy 
> > constructor on Bio::Seq::RichSeq that accepts Bio::PrimarySeqs (or 
> > whatever) then you would 'upgrade'.
> > 
> > 	-hilmar
> OK, I see.
> Something like:
> 1) deep copying 
> use Bio::SeqIO;
> my $gbio = Bio::SeqIO->new(-format => 'genbank');
> 
> while (my $seq1 = $gbio->next_seq)
> {
>   my $seq2 = $seq1->copy # $seq2 is deep copy of Bio::Seq::RichSeq object
> $seq1
> 
>   # do some stuff with $seq2
> }
> 
> or:
> 2) 'upgrading'
> use Bio::SeqIO;
> use Bio::Seq::RichSeq;
> my $fasta_io = Bio::SeqIO->new;
> 
> while (my $seq1 = $fasta_io->next_seq)
> {
>    my $seq2 = Bio::Seq::RichSeq->copy($seq1) # $seq2 is enriched fasta seq
> object
> 
>    # do some stuff with $seq2
> }
> 
> Correct ?
> Marc
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________