[Bioperl-l] GFF file and load_gff.pl

Lincoln Stein lincoln.stein at gmail.com
Wed Jan 28 14:37:33 EST 2009


You may want to add the -c flag to the bp_load_gff.pl command line in order
to create the GFF schema. This will be independent of the biosql schema.

Lincoln

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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-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>


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