[Bioperl-l] GFF file and load_gff.pl

Scott Cain scott at scottcain.net
Wed Jan 28 11:15:20 EST 2009


Hi Richard,

Your mixing up two database schemas.  Do you want to use a BioSQL
database (bioperl-db) or a Bio::DB::GFF database?  I'm guessing that
you want the latter, so I'll answer that question (as it's the easier
one anyway).  You need to add the "-c" flag (for --create) to the
load_gff.pl command to create the Bio::DB::GFF schema.

If you really wanted a BioSQL database, you'll have to wait for help
from someone else more knowledgeable about it.

Scott




On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison
<richard.harrison at ed.ac.uk> wrote:
> Dear all,
>
> I am running Bioperl 1.6 on osx- leopard on a macbook pro.
>
> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the
> biosql-schema for mysql and bioperl-db.  As per the instructions I have a
> database called biosql which I associated the SQL dialect biosqldb-mysql.sql
>
> After much fannying, the install seems fine....although i can't be sure
> (never used mysql before)
>
> I am having problems with the script load_gff.pl
>
> I want to load  a database with the data from a genome.gff file (for
> saccharomyces cerevisiae). I don't want to add sequence to it, as all i need
> is the annotation.
>
> I have tried the following command(s):
>
> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff
>  ./bp_load_gff.pl -d biosql -user root -pass mypassword --adaptor=dbi::mysql
>  genome.gff
>
> With both I get the following error:
>
> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped.
> (then another few '000 of these)
> then..
>
> genome.gff: 16379 records loaded
>
>
> Any ideas where I'm going wrong?
>
> Thanks,
>
> Richard
>
> ____________________________
> Dr Richard Harrison
> 127 Ashworth Labs
> Institutes of Evolutionary Biology
> King's Buildings
> West Mains Road
> Edinburgh EH9 3JT
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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