[Bioperl-l] swissprot under mysql

[David Guzman]

The error was solved, it seemed it dealed more with MySQL than bioperl 
itself, I uninstalled and reinstalled cleanly MySQL server, killing 
inmediately safe_mysqld and mysqld processes, due to rpm starts these servers 
inmediately after installation, then the edition of my.cnf and the change of 
var/lib/mysql to other partitions were effective. I performed all types of 
queries under MySQL and all works, now I have to check querying under bioperl.

                                             David

pd: thanks to chris mungall and hilmar lapp

On Wednesday 28 August 2002 9:04 pm, Hilmar Lapp wrote:
> Which versions of bioperl-db and bioperl do you run? (You should run
> a recent cvs snapshot from bioperl-db, and bioperl-1.1.x - bioperl
> 1.0.x will not work).
>
> The error that you see is most likely due to a slot being undef when
> it is not expected to be (because the code constructs the SQL itself
> instead of binding parameters). If the error does not go away with
> the aforementioned versions, it'd be helpful if you can track down
> the swprot accession that causes the error.
>
> 	-hilmar
>
> On Saturday, August 24, 2002, at 11:16  AM, David Guzman wrote:
> > Hello:
> >
> > Thanks to Chris Dagdigian and Keith Allen for the information
> > provided in
> > this list, allowing me to get to this point...
> >
> > I am trying to load protein databases under MySQL, I followed up the
> > indications appearing in BioTeam.Net HOWTO #1 "MyGENBANK with MySQL"
> > but load_seqdatabase.pl script throws me the following error message (3
> > seconds later):
> >
> > #./load_seqdatabase.pl -host localhost -sqldb biosqlsw -dbuser root
> > -dbpass
> > <....> -format swiss swissprot40
> > /usr/site/databases/seqdb/swissprot/sprot40.dat
> > Reading /usr/site/databases/seqdb/swissprot/sprot40.dat
> > DBD::mysql::st execute failed: You have an error in your SQL syntax
> > near ')'
> > at line 1 at
> > /usr/lib/perl2/site_perl/5.6.1/Bio/DB/SQL/SeqLocationAdaptor.pm
> > line 369, <GENO> line 85.
> >
> > It is a different problem than the one described by Keith Allen, I have
> > already adjusted max_allowed_packet, sort_packet and record_buffer
> > to 3M as
> > suggested
> >
> > Any idea???... thanks for your help
> >
> >
> >                                                       David Guzman
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