[Bioperl-l] swissprot under mysql

[Hilmar Lapp]

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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>
--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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