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

[Anja F. <fri...@ho...>]

My bad, I created the config file long time ago and forgot to have alook into it again ;(
By the way, where did you get the code for the colours in the css file from? Wikipedia is using different ones... and can JBrowse display any colour? As I have to display 12 small motifs I'm running out of colours...
Thanks for your help

Anja
Date: Thu, 30 Sep 2010 02:20:44 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
  
  
    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