[Bioperl-l] Pulling down data from NCBI

[Mgavi Brathwaite]

What "cookbook"?

Mgavi

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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>
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