[Bioperl-l] GFF file and load_gff.pl
richard.harrison at ed.ac.uk
Wed Jan 28 15:22:02 UTC 2009
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 --
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
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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