[Bioperl-l] RE: [Gmod-gbrowse] Some minor bugs/observations

[Lincoln Stein]

I just added a primary_seq() method to Bio::DB::GFF::Segment.

Lincoln

On Monday 24 March 2003 04:08 pm, Marc Logghe wrote:
> Hi Korine,
> I'd like to address at least one issue
>
> > 1) The "Dump Sequence" plug-in doesn't work for EMBL and
> > BSML(XML) formats.
>
> The EMBL output is broke because a primary_seq method is missing. My most
> recent BatchDumper.pm revision contains the following stab:
>     # this one is necessary to make EMBL output work
>     local *Bio::DB::GFF::Segment::primary_seq = sub {
>         my $self = shift;
>     };
> I did not check BSML output, however. Be sure to have the necessary non
> Bioperl modules to enable that (XML::Parser)
>
> > 2) Entering a sequence range in reverse order gives wonky results.
> > 3) Entering out-of-range sequence numbers doesn't give an
> > error message (it
> > would be nice if it did)
> > 4) The track labels for remote annotations don't show up if
> > they're not in
> > the current display range (it would be nice if they did)
> > 5) Navigation using browser buttons can get a little
> > frustrating. Is there
> > any way to put some navigation buttons on the mainpage?
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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