[Bioperl-l] Pulling down data from NCBI

[Abhishek Pratap]

Thank you guys for very quick responses.  My bad I trusted my fingers.

Now that this is working the output that I am getting is not what I
want. I am sure I am missing the correct way of doing it. So If I
search the Nucleotide db @NCBI for this accession number "
AAPP01000000", I see some 34 k records. What I need to do is pull down
those sequences as fasta files.

I am referring to
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook  but dint quite
find a similar example.

Thanks!
-Abhi

On Mon, Feb 1, 2010 at 3:39 PM, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:
> 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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>