[Bioperl-l] Re: Best method for downloading 100 sequences

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Fri Sep 2 14:12:40 EDT 2005

Hi Amir,

I've done it before by using a loop without sleep() for the EMBL-Bank 
and it works fine. I use an input file with all the sequence ID's 
organized by gene/allele name so all the downloaded files get into 
corresponding directories. I can send you the code if you want to adjust 
it to your needs.


--- Amir Karger <akarger at CGR.Harvard.edu> wrote:
 > Hi.
 > I'm using Bioperl's nice get_sequence in my Scriptome toolbox, to
 > fetch a single sequence. What would be the best method for downloading
 > 100 sequences? Do I write a loop to call get_sequence N times? Will
 > the various websites get angry at me for doing that? Would they be
 > less angry if I did a 1-second sleep after each download? I know NCBI
 > has methods to pull in N sequences, but I don't know whether Swiss et
 > al. do too. I'm happy to use other Bioperl code, rather than
 > get_sequence. I just need to have a script that people can cut and
 > paste, where they just input the filename with sequence IDs and the
 > database to download from (sort of like
 > a_popular_internet_database__fetch_sequence_web_)
 > Thanks,
 > -Amir Karger

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

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