[Bioperl-l] Pulling down data from NCBI

[Folmer Fredslund]

Hi Mgavi,


On 2 February 2010 16:40, Mgavi Brathwaite <lsbrath at gmail.com> wrote:
> What "cookbook"?
>
> Mgavi
>

I don't know much about BioPerl yet, but merely searching for
"ncbi eutilities cookbook"
on google gave me this site
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

I would guess this is the page referred to.

This is just me saying: Please use 2min to get your own answers before
you ask everybody on this list.

Best regards,
Folmer Fredslund



> On Mon, Feb 1, 2010 at 4:31 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
>> Abhi,
>>
>> The accession in question is for a record containing a set of sequences,
>> not just one sequence (it's a contig record).  The NCBI web interface is
>> performing an esearch on this to get 34K seqs, the equivalent with
>> EUtilities is:
>>
>> ================================
>> use Bio::DB::EUtilities;
>>
>> my $id = 'AAPP01000000[ACCN]';
>>
>> my $factory = Bio::DB::EUtilities->new  (
>>        -eutil =>  'esearch',
>>       -db    =>  'nucleotide',
>>       -term  =>  $id,
>>       -usehistory => 'y');
>>
>> say $factory->get_count;
>>
>> # do more here...
>>
>> ================================
>>
>> The 'do more here' part is covered in the cookbook, and will require you
>> retrieving the seqs in chunks.
>>
>> chris
>>
>> On Feb 1, 2010, at 2:45 PM, Abhishek Pratap wrote:
>>
>> > 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
>> >>> _______________________________________________
>> >>> Bioperl-l mailing list
>> >>> Bioperl-l at lists.open-bio.org
>> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >>>
>> >>
>> >
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