[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- 

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  
(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.

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