[Bioperl-l] Batch retrieval partially implemented inBio::DB::GenBank/GenPept

[Mauricio Herrera Cuadra]

hehehe :)

Chris Fields wrote:
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Chris Fields
>> Sent: Wednesday, May 03, 2006 4:10 PM
>> To: 'Jason Stajich'; 'Brian Osborne'; bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Batch retrieval partially implemented
>> inBio::DB::GenBank/GenPept
>>
>> Just wanted to let you guys know I have added a few bits and pieces to
>> Bio::DB::Gen*  and BioLLDB::NCBIHelper for batch retrieval using
>                      ^^^^^^^^^^^^^^^^^^^
>                      Bio::DB::NCBIHelper
> Fat fingers!
> 
>> epost/efetch.  I didn't want to break anything too severely so you can
>> only
>> use this at the moment using get_seq_stream (i.e. NOT through get_Stream*
>> methods yet).  I also added tests to DB.t, a few each for protein and
>> nucleotide retrieval using batch mode and so far they all pass fine.
>>
>> I haven't tested the upper sequence limit for this yet to see if it's at
>> all
>> comparable to just using efetch but it seems a bit faster.  The eutils
>> coursebook states that one should only post ~500 at a time (I think you
>> can
>> get a bit higher though).
>>
>> Also, at the moment it only works at the moment for GI's (NOT accessions,
>> which apparently epost does not accept).  If we want to continue using
>> this
>> method for retrieval then we may need a workaround for accs.
>>
>> CJF
>>
>> Christopher Fields
>> Postdoctoral Researcher - Switzer Lab
>> Dept. of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM