[Bioperl-l] NCBI efetch: request limits and getting dates fast

Dave Messina David.Messina at sbc.su.se
Tue Apr 20 17:48:41 EDT 2010


Great, thanks Chris, I'll try it that way.

Dave



On Apr 20, 2010, at 8:57 PM, Chris Fields wrote:

> Not sure about the upper limit with SOAP, but simple ol' EUtilities can take ~250-500 IDs (somewhere in that range) with a direct efetch/esummary/elink, and many many more if you use epost first.  I have been able to fetch a couple thousand with epost.  
> 
> As an example, this code works for me:
> 
> use Modern::Perl;
> use Bio::DB::EUtilities;
> 
> my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
>                                     -db    => 'protein',
>                                     -email => 'cjfields at bioperl.org',
>                                     -term  => 'pyrR',
>                                     -retmax => 250,
>                                     -usehistory => 'y');
> 
> my $hist = $eutil->next_History || die "No history returned";
> 
> $eutil->set_parameters(-eutil => 'esummary',
>                       -history => $hist);
> 
> my %id_map;
> 
> while (my $ds = $eutil->next_DocSum) {
>    my ($cdate) = $ds->get_contents_by_name('CreateDate');
>    $id_map{$ds->get_id} = $cdate;
> }
> 
> say join("\t", $_, $id_map{$_}) for sort keys %id_map;



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