[Bioperl-l] Question about BioPerl Bugzilla Bug 2213

Chris Fields 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  
cases.  The
issue is directly related to recent changes in Bio::Species and and  
could be
taken care of by simply not running any postprocessing and foregoing the
lineage checking altogether in Bio::Species::classification(), where the
exception occurs.

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  
can comment?"

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  
demonstrates).

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?

chris

On Mar 27, 2007, at 3:42 PM, Carrel, Michael, G wrote:

> Chris,
>
>
>
> 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[0]->[0] = $obj->binomial();  ).
>
>
>
> Thank you,
>
>
>
> Mike Carrel
>
> Network Analyst
>
> 816-234-1571
>
> mgcarrel at cmh.edu
>
> <image001.png>
>
>
>
> <image001.png>
> <Carrel, Michael, G.vcf>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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