[Bioperl-l] GFF file and load_gff.pl
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
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.
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
> 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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