Hello,
It looks like we should add an example to the tutorial for using
flatfile-to-json.pl, and flatfile-to-json.pl probably needs some changes
or at least more helpful error messages.
Could you send your gff file and your data/refSeqs.js file? That should
help me reproduce the problem you're seeing.
Thanks,
Mitch
On 09/24/2009 06:06 AM, Adhemar wrote:
> Hi All,
> I'm a newbie on using jbrowse and I'm quite excited with its
> functionalities.
> The installation ran smoothly and it's working 100% if I follow the
> 'Getting Started With JBrowse' tutorial.
> The thing is that I couldn't create a new jbrowse instance using a GFF
> file.
> It's not working even with the example file (volvox.gff).
> I wonder if you could help me figure out what's going on.
> My PC is a Fedora 11 i386 + bioperl 1.6 + JSON 2.15.
> Here is the error message:
>
> [localuser@localhost temp]$ bin/flatfile-to-json.pl -gff file.gff
> --autocomplete all
>
> working on seq Seq1
>
> -------------------- EXCEPTION --------------------
> MSG: segment() called in a scalar context but multiple features match.
> Either call in a list context or narrow your search using the -types or
> -class arguments
>
> STACK Bio::DB::SeqFeature::Store::segment
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store.pm:1298
> STACK toplevel bin/flatfile-to-json.pl:152
> -------------------------------------------
>
>
> Thanks in advance.
> Adhemar
>
|
