[Bioperl-l] Pulling down data from NCBI

[Kevin Brown]

Looks like you've misspelled one of the parameters. It should be
'efetch' not 'efecth'

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Abhishek Pratap
> Sent: Monday, February 01, 2010 1:36 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Pulling down data from NCBI
> 
> Hi All
> 
> I looking to batch download some 34K nucleotide sequences,
> corresponding to a NCBI accession number. I tired the following and
> getting an error. Has it got anything to do with recent update to code
> that Chris was discussing.
> 
> 
> 
> my $factory = Bio::DB::EUtilities->new  (
> 					-eutil	=> 'efecth',
> 					-db 	=>	'nucleotide',
> 					-retype	=>	'fasta',
> 					-id		=> $id
> 				);
> 
> 
> ----------- EXCEPTION: Bio::Root::Exception -------------
> MSG: efecth not supported
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:357
> STACK: Bio::Tools::EUtilities::EUtilParameters::eutil
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
> ameters.pm:452
> STACK: Bio::Root::RootI::_set_from_args
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Root/RootI.pm:546
> STACK: Bio::Tools::EUtilities::EUtilParameters::new
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Tools/EUtilities/EUtilPar
> ameters.pm:193
> STACK: Bio::DB::EUtilities::new
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/EUtilities.pm:74
> STACK: ./getDatafromNCBI.pl:9
> 
> 
> -Abhi
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