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

[Brian Osborne]

Korine and Marc,

>I did not check BSML output, however. Be sure to have the necessary non
>Bioperl modules to enable that (XML::Parser)

Minor detail, excuse my nitpicking. SeqIO::bsml.pm uses XML::DOM, not
XML::Parser. I'll update INSTALL.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Marc Logghe
Sent: Monday, March 24, 2003 4:09 PM
To: 'korineu at sfu.ca'
Cc: Bioperl (E-mail)
Subject: [Bioperl-l] RE: [Gmod-gbrowse] Some minor bugs/observations

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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