[Bioperl-l] GFF file and load_gff.pl

Adam Witney awitney at sgul.ac.uk
Wed Jan 28 11:34:59 EST 2009


I am not an expert on mysql but it looks to be complaining that the  
table biosql.ftype doesn't exist. Can you verify that the table is in  
the database?

Previously when i set this up i used bulk_load_gff.pl with the -- 
create option to first create the table structure in the database.

HTH

adam

On 28 Jan 2009, at 15:22, 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
>
> ____________________________
> 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
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list