Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Mitch S. <mit...@be...>]

  You're right that if you use Bio::DB::SeqFeature::Store then you don't 
need to use chado.  But it looks like the config file you're using with 
prepare-refseqs.pl might still refer to Bio::DB::Das::Chado?  If you 
change that to Bio::DB::SeqFeature::Store in the config file, then that 
should help.

Mitch

On 09/30/2010 02:13 AM, Anja Friedrich wrote:
> Hi,
>
> I loaded the lemna data with bp_seqfeature_load.pl into the database 
> and wanted to use bin/prepare-refseqs.pl for the reference sequence. 
> But I get:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: unable to find SO or SOFA in the database!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw 
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::DB::Das::Chado::sofa_id 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
> STACK: Bio::DB::Das::Chado::new 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
> STACK: bin/prepare-refseqs.pl:115
> -----------------------------------------------------------
> Could not open database:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: unable to find SO or SOFA in the database!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw 
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::DB::Das::Chado::sofa_id 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
> STACK: Bio::DB::Das::Chado::new 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
> STACK: bin/prepare-refseqs.pl:115
> -----------------------------------------------------------
>
> How can that be? I thought if I use Bio-SeqFeature-Store I dont need a 
> database like Chado to store the data? Is there somewhere a 
> description where I can read more about it and reference sequences?
>
> Anja