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

[boileau at essi.fr]

Thanks, your fix worked :)

William Boileau


> 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
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