[Bioperl-l] Mixed bless-ings with Bio::Seq/Bio::PrimarySeq (Bio::Seq::Meta::Array)

Michael Kiwala mkiwala at watson.wustl.edu
Thu Apr 5 15:11:22 EDT 2007


My vote is for SeqI.

I was using the SeqWithQuality class and more recently switched over to 
Bio::Seq::Quality as we are upgrading from 1.4 to 1.5.2. The sequences 
I'm working with are destined for GenBank and have features and quality 
values. I've written a module (that I call GenBank::Tbl2Asn) that 
accepts a Bio::Seq::Quality with features and runs tbl2asn on it to 
produce a file that we send to GenBank. I don't know of any other class 
that suites my needs better than Bio::Seq::Quality inheriting from 
Bio::SeqI.


Chris Fields wrote:
> I tend to agree on that front as it seems too prone to subtle issues  
> with inheritance (as the bug demonstrates).
>
> Related to that, do we want to have Bio::Seq::Meta::Array implement  
> either PrimarySeqI or SeqI?  Having it implement both is definitely  
> not working as expected.
>
> chris
>
> On Apr 5, 2007, at 1:27 PM, Hilmar Lapp wrote:
>
>   
>> On Apr 5, 2007, at 1:40 PM, Chris Fields wrote:
>>
>>     
>>> Do we want to support using 'bless $obj, Class'
>>>       
>> This smacks of over-clever programming and looks like a sure way to  
>> obfuscate what you're doing. I'm not sure why we need to support  
>> this construct.
>>
>> 	-hilmar
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>>     
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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