Re: [GMOD-devel] GBROWSE:Computed options for link

[Jason S. <ja...@cg...>]

I get this error with the current checkout version:
[Fri Dec 20 11:56:17 2002] [error] Variable length lookbehind not implemented before HERE mark in regex m/(src|h
ref)="(?<!(http:|ftp:))([^"\#\$]+)" << HERE / at /var/www/perl/gbrowse line 1967.

running perl 5.6.1


On Thu, 19 Dec 2002, Oliver Burren wrote:

> Lincoln,
>
> Thanks very much for fixing the comment bug. I have fixed the other
> problem which was down to me I have to admit. I have a small suggestion:
> Would it be possible to add a way of including hypertext links in the
> citation as well as text. Something like adding
>
> $citation=~ s!\b((http|ftp)://[^ ]*)!<a href=\"\1\">\1<\/a>!g;
>
> to the make_citation subroutine before the return ? Please feel free to
> ignore if it is a bad idea.
>
> Thanks very much for your help and festive greetings.
>
> Olly
>
>
> On Fri, 13 Dec 2002, Lincoln Stein wrote:
>
> > Sorry it's taken me so long to respond, but this got lost in my inbox.  The
> > problem with comment characters has now been fixed.  I cannot reproduce the
> > issue with the attribute handling, but agree that  aggregation is the prime
> > suspect.  Do each of the exons carry the EnsEMBL_Gene_ID attribute?
> >
> > Lincoln
> >
> >
> > On Thursday 05 December 2002 10:45 am, Oliver Burren wrote:
> > > Hi,
> > >
> > > I want to link from stored EnsEMBL Transcripts to the Ensembl geneview
> > > page directly. Currently the features that make up these transcripts are
> > > stored as exons
> > > eg.
> > >
> > > Landmark	EnsEMBL	exon	501     663     .       1       .
> > > Transcript "ENSMUST000000XXXX"; EnsEMBL_Gene_ID "ENSMUSG00000XXXX"
> > >
> > > Obviously for aggregation to work correctly I have to keep 'Group' as
> > > Transcript, however I hoped to 'compute' the link required as follows
> > >
> > > link = sub {
> > > 	my $feature=shift;
> > > 	my $id=$feature->attributes('EnsEMBL_Gene_ID');
> > > 	return "http://www.ensembl.org/geneview?gene=$id";
> > > 	}
> > > However this doesn't seem to work. I thought maybe it was due to an
> > > aggregation problem so I wrote a small perl script to test things out.
> > >
> > > use Bio::DB::GFF;
> > > my $db = Bio::DB::GFF->new(-adaptor => 'dbi::mysqlopt',
> > >                         -dsn => 'dbi:mysql:somedb:somwhere',
> > >                         -aggregator => 'transcript',
> > >                         -user => noone);
> > > my $landmark=shift;
> > > my $segment = $db->segment($landmark);
> > > my @transcripts=$segment->features('transcript');
> > > foreach (@transcripts){
> > >         my $gene_id = $_->attributes('EnsEMBL_Gene_ID');
> > >         print "EnsEMBL gene is $gene_id\n";
> > > }
> > >
> > >
> > > This seems to work a treat. Does anyone know what is going on I'm using
> > >
> > > perl v5.6.1 built for i686-linux
> > > bioperl-1.0.2
> > > Gbrowse 1.47
> > > I'm not using mod_perl at the moment
> > >
> > > Also by the by I don't think gbrowse likes you using comments in your
> > > code in the computed options! Has anyone else encountered this ?
> > >
> > > Any help greatly appreciated,
> > >
> > > Olly
> > >
> > >
> > >
> > > -------------------------------------------------------
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> > > _______________________________________________
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> >
> > --
> > Lincoln Stein
> > ls...@cs...
> >
> >
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu