[Bioperl-l] GFF file and load_gff.pl

Chris Fields cjfields at illinois.edu
Wed Jan 28 11:28:25 EST 2009


On Jan 28, 2009, at 9:22 AM, Richard Harrison 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

Yes.  You are confusing a BioSQL database with a Bio::DB::GFF database  
(see the documentation for load_gff.pl, it mentions Bio::DB::GFF, not  
BioSQL).  So, the errors may be popping up b/c you're mixing two db  
schemas.

chris



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