[Bioperl-l] GFF file and load_gff.pl

Richard Harrison richard.harrison at ed.ac.uk
Wed Jan 28 10:22:02 EST 2009


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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