[Bioperl-l] Re: entrezgene binary ASN

[Stefan Kirov]

Yes, Hilmar is right- there should be Bio::Index::entrezgene to do that. 
I agree this functionality is better kept separated from Bio::SeqIO parser.
Stefan

Hilmar Lapp wrote:

>
> On Oct 2, 2005, at 8:27 AM, Michael Seewald wrote:
>
>> On 10/2/05, Hilmar Lapp <hlapp at gmx.net> wrote:
>>
>>>
>>>
>>> On Oct 1, 2005, at 1:01 PM, Stefan Kirov wrote:
>>>
>>>> Hilmar,
>>>> As of now the parser does not seek through the streem, but hopefully
>>>> it will as soon as I can sit down and do it
>>>
>>>
>>> What advantage would that have?
>>
>>
>>
>>
>> You could create an index and seek by gene id. Could be handy in some 
>> cases,
>> although I wouldn't use it (personally).
>>
>> [...]
>>
>> The "streaming use" shouldn't be affected. BTW, there are other bioperl
>> modules that use indices.
>
>
> Right, but they use a different implementation (module) for indexing, 
> not the SeqIO parser (it only parses the entry).
>
>     -hilmar
>
>
>> Best wishes,
>> Michael
>>
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>>
>>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
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