[Bioperl-l] Question about BioPerl Bugzilla Bug 2213
cjfields at uiuc.edu
Tue Mar 27 17:17:51 EDT 2007
First, you should direct this to the mail list in case anyone else
can add to this. I may not be able to get to this anytime real soon.
From the bug report:
"The postprocessing in SpeciesAdaptor does mess things up in some
issue is directly related to recent changes in Bio::Species and and
taken care of by simply not running any postprocessing and foregoing the
lineage checking altogether in Bio::Species::classification(), where the
However, I believe doing so may break functionality with older
bioperl-db/BioSQL installations since data is stored based on the older
Bio::Species system (single-name genus and species). Maybe Hilmar
As noted in the bug report this is still considered a developer
series; even though most of the core modules work well together there
are still some interoperability issues present (as this bug
Maybe having a BioSQL TaxonAdaptor module would be a workaround;
Bio::Species is-now-a Bio::Taxon (whereas pre-1.5.2 versions aren't),
so if we had a module that stored data in the newer context it might
work around this. Hilmar?
On Mar 27, 2007, at 3:42 PM, Carrel, Michael, G wrote:
> I am trying to apply this patch to my BioPerl-DB 1.5.2 code and
> don't understand what the changes are in the Bio/DB/BioSQL/
> SpeciesAdaptor.pm code. What does the "+=pod" text mean? Same for
> "+=cut"? Are we commenting out lines 256 through 280?
> The text says that "massaging" code was commented out, but I don't
> understand exactly what lines are commented out. Please explain in
> more detail what the changes are in the SpeciesAdaptor.pm file.
> I believe I understand the changes in the Bio/DB/BioSQL/mysql/
> SpeciesAdaptorDriver.pm code file...commenting out the one line
> ( #$clf-> = $obj->binomial(); ).
> Thank you,
> Mike Carrel
> Network Analyst
> mgcarrel at cmh.edu
> <Carrel, Michael, G.vcf>
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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