[Bioperl-l] type=MyISAM & regression in Bio::DB::GFF

[Scott Cain]

Hi Lincoln,

Sorry about the sloppy <> operator.  I was thinking of using it to "hit return to continue" but I didn't think too carefully about the context.  In retrospect, I don't think it should do that anyway, since if anybody is using one of the loaders in a pipeline, it would break it.  Thanks for fixing it.

Scott


Sent from my iPad

On 2011-04-01, at 10:57 AM, Lincoln Stein <lincoln.stein at gmail.com> wrote:

> Hi Scott,
> 
> I've fixed bioperl live's Bio::DB::GFF type=MyISAM problems, so it will now work correctly on recent Mysqls. During testing of this, I found a regression that you had apparently introduced when you added a warning message about loading GFF3 files:
> 
> sub print_gff3_warning {
>   my $self = shift;
>   print STDERR <<END
> 
> You are loading a Bio::DB::GFF database with GFF3 formatted data.
> While this will likely work fine, the Bio::DB::GFF schema does not
> always faithfully capture the complexity represented in GFF3 files.
> Unless you have a specific reason for using Bio::DB::GFF, we suggest
> that you use a Bio::DB::SeqFeature::Store database and its corresponding
> loader, bp_seqfeature_load.pl.
> 
> END
> ;
> 
> my $h = <>;
> 
>   return;
> }
> 
> The <> was gobbling up the very next line in the GFF3 file, regardless of what its contents were. Was there some reason for you to want this behavior, or were you trying to discard the ##gff-version line? In any case, this broke regression tests, so I've removed it. Let me know what was the intent, if I'm missing something.
> 
> Lincoln 
> 
> On Thu, Mar 31, 2011 at 6:59 PM, Scott Cain <scott at scottcain.net> wrote:
> Hi Lincoln,
> 
> It appears that having "type=MyISAM" in the table definitions for
> newer MySQL instances is a problem, as I get this when I try to create
> a Bio::DB::GFF database:
> 
> You have an error in your SQL syntax; check the manual that
> corresponds to your MySQL server version for the right syntax to use
> near 'type=MyISAM' at line 6 at
> /Library/Perl/5.8.8/Bio/DB/GFF/Adaptor/dbi.pm line 1049.
> 
> Should we change that, or is there a way to get newer mysql servers to
> accept it as is?
> 
> Thanks,
> Scott
> 
> 
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> 
> 
> -- 
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>