[Bioperl-l] possible bug printing GenBank feature qualfiers

Scott Markel smarkel at scitegic.com
Mon Apr 3 12:28:09 EDT 2006


Chris,

Apologies again that my simplistic input file caused confusion.
Thanks for making the CVS changes.

Scott

Chris Fields wrote:

> Removed Scott's line from Bio::SeqIO::genbank in CVS (reverted back  to 
> the previous version); it's much simpler that way and we avoid an  extra 
> method call.  Sorry about all the confusion here; I was worried  that 
> the parsing issue I was seeing about the feature flag had  something to 
> do with Scott's bug when they were completely unrelated.
> 
> Chris
> 
> On Apr 1, 2006, at 3:34 AM, Hilmar Lapp wrote:
> 
>>
>> On Mar 31, 2006, at 8:26 PM, Chris Fields wrote:
>>
>>> Since the problem seems to be solved and both fixes (Scott's and
>>> Heikki's) are redundant and essentially get the same results, one of
>>> them should be rolled back.
>>
>>
>> Please don't leave the line
>>
>>     $value = $value->{"value"};
>>
>> Either remove it (because the problem needs to either be 'fixed' in  all
>> writers, or at the root), or if you want to leave this construct in,
>> protect it with a conditional and use the method-based access as I  sent
>> an example before.
>>
>>     -hilmar
>> -- 
>> ----------------------------------------------------------
>> : Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
>> ----------------------------------------------------------
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> 
> 

-- 
Scott Markel, Ph.D.
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