[Bioperl-l] Using Storable with SeqFeatures

[Hilmar Lapp]

On Sep 24, 2008, at 10:19 AM, Johnston, Caroline wrote:

> Hello.
>
> I'm trying to use Storable to save a Bio::Seq object and Storable  
> seems to be having a weird problem dealing with freezing and thawing  
> the code ref to Bio::SeqFeature::Generic cleanup_generic. If I  
> change one line (931) in that function from
>
>    foreach my $t ( keys %{$self->{'_gsf_tag_hash'} || {} } ) {
>                                                    ------
> to
>
>    foreach my $t ( keys %{$self->{'_gsf_tag_hash'} } ) {
>
> it works fine. I've pasted an example script at http://sial.org/pbot/32320 
> .
>
> Any ideas why this syntax would break Storable? Would wrapping the  
> foreach in an if(defined $self->{'_gsf_tag_hash'}) serve to replace  
> the || {} ?

This should have exactly the same behavior as far as I can see.

Would you mind filing this as a bug repot with patch?

	-hilmar

>
>
> I get the same problem using Bio::Root::Storable.
>
> Cxx
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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