[Bioperl-l] GFF file and load_gff.pl
scott at scottcain.net
Wed Jan 28 11:15:20 EST 2009
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.
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
> 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)
> genome.gff: 16379 records loaded
> Any ideas where I'm going wrong?
> Dr Richard Harrison
> 127 Ashworth Labs
> Institutes of Evolutionary Biology
> King's Buildings
> West Mains Road
> Edinburgh EH9 3JT
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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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