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

Lincoln Stein lincoln.stein at gmail.com
Fri Apr 1 16:57:19 UTC 2011

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.


my $h = <>;


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.


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>

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