[Bioperl-l] A Bio::Graphics/Bio::Seq problem

[Jason Stajich]

On Thu, 30 Jan 2003 boileau at essi.fr wrote:

> I asked the problem last week, but had no answers... Sorry to ask it
> again, but I really don't know why it doesn't work... :-\

Because there is an incompatibility in the object model that Lincoln was
using and Bio::PrimarySeqI when Bio::RangeI was removed from the
interface.


> With the code below, I have the following error :
>
> Can't locate object method "start" via package "Bio::Seq" at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Graphics/Panel.pm line 45,<DATA> line 141.
>
> When I change the type of the SeqFactory, the error is different (the
> package is "Bio::PrimarySeq" instead of "Bio::Seq" when I leave the type
> unchanged), but since the code is the same as the one in the
> documentation, I don't understand the problem...Forgot to say, the object
> $hit is "good".Thanks for your help !
>

Short term fix:
my $factory = new Bio::Seq::SeqFactory(-type => 'Bio::LocatableSeq');


> William Boileau
>
>
>
> @hsps = $hit->hsps();
>
> my $factory = new Bio::Seq::SeqFactory(-type => 'Bio::Seq');
>
> foreach my $hsp(@hsps) {
>   $query_string = $hsp->query_string;
>   $seq = $factory->create(-seq => $query_string,
>                             -id  => 'name');
>
>
>  my $panel = Bio::Graphics::Panel->new(
>                                        -segment   => $seq,
>                                        -key_style => 'between',
>                                        -width     => 800,
>                                        -pad_left  => 10,
>                                        -pad_right => 10,
>                                        -start => 1,
>                                        );
> }
>
>
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu