[Bioperl-l] Bio::Variation::SeqDiff, Bio::Variation::VariantI

[Heikki Lehvaslaiho]

Eckhard,

Your idea looks good on paper. Go ahead and try it. 

I have not touched these classes for a while. The current functionality was
enough for my needs. You are welcome to develop them further as long as you
do not changed existing methods too drasticly. ;-)

Yours,
	-Heikki


Eckhard Lehmann wrote:
> 
> Hi,
> 
> as I know, I can create a Bio::Variation::DNAMutation and add alleles
> and other things to it, e.g. an "upStreamSeq" or a "dnStreamSeq".
> Then I can add the Bio::Variation::DNAMutation to a
> Bio::Variation::SeqDiff container and besides that I can set a sequence
> as dna_ori respectively dna_mut to the Bio::Variation::SeqDiff
> container.
> 
> OK, that's fine ;-). But I wonder why I don't get the dna_mut sequence
> automatically when all DNAMutation objects and the dna_ori sequence are
> set correctly?
> Has there anything been done into this direction since bioperl-1.0? When
> not, I'd like to implement such a method:
> 
> #------------------------------
> sub dna_mut {
>   my ($self, $sq) = @_;
> 
>   return $self->{'dna_mut'} unless ($sq && $self->{'dna_mut'});
> 
>   if (!$sq && $self->{'dna_ori'}) {
>     my $sq
>     foreach ($self->each_Variant) {
>       next unless $_->isMutation;
> 
>       my $sub_ori = $_->dnStreamSeq . $_->allele_ori . $_->upStreamSeq;
>       my $sub_mut = $_->dnStreamSeq . $_->allele_mut . $_->upStreamSeq;
>       ($sq = $self->{'dna_ori'}) =~ s/$sub_ori/$sub_mut/;
>     }
>   }
>   $self->{'dna_mut'} = $sq;
> }
> #------------------------------
> 
> or like this...
> It is not tested and I don't know whether it would work...
> 
> Is it a good idea to change the dna_mut method that way in the public
> BioPerl?
> 
> Thank you for suggestions and answers
> 
> Eckhard
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@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
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