[Open-bio-l] Agreed name for UniProt XML file format

Hilmar Lapp hlapp at drycafe.net
Tue Jul 27 14:57:33 EDT 2010


On Jul 27, 2010, at 12:14 PM, Chris Fields wrote:

>> P.S. Chris, am I right in thinking that if BioPerl were to support  
>> this
>> file format under the name "uniprot-xml" this would be equivalent
>> to accepting format="uniprot" and variant="xml"? And furthermore
>> and assuming you regard this as the default/only variant, Bio::SeqIO
>> would also just accept format="uniprot"?
>
> In cases where 'uniprot' is passed, we could handle it either way:  
> delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an  
> alias of 'swiss'), or always use the XML handler for 'uniprot' and  
> ignore the variant argument.  Either way is fine with us.


Frankly I'm afraid to most people uniprot as a format name is  
synonymous with swiss(prot). So that should probably be the default  
(rule: the default should always be the least surprising choice).

Alternatively, can we auto-detect whether it is XML without messing up  
an XML parser if the input is coming from a pipe?

	-hilmar
-- 
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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