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

Chris Fields cjfields at illinois.edu
Tue Apr 20 23:32:12 EDT 2010


Interesting, that's essentially what the example I sent did, just with the standard eutils interface.  Would be interesting to see how the two compare.

chris

On Apr 20, 2010, at 8:30 PM, Mark A. Jensen wrote:

> Hey Dave-- I think you've got to set
> 
> -RetMax => 250
> 
> in the fetch call.
> 
> To get the date without the other stuff, you might try working with docsums instead of sequences. It's been a while, so I'm fuzzy on the details (and the details are fuzzy anyway). Can you send a gist of your code?
> MAJ
> ----- Original Message ----- From: "Dave Messina" <David.Messina at sbc.su.se>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Tuesday, April 20, 2010 1:22 PM
> Subject: [Bioperl-l] NCBI efetch: request limits and getting dates fast
> 
> 
> Hi everyone,
> 
> I've got about 250 NCBI IDs that I'm pulling from NCBI using Bio::DB::SoapEUtilities. It works fine if I send 10 IDs at a time, but much more than that and I get an 'unspecified internal server error'.
> 
> I thought the limit with 500 IDs at a time — anyone have an idea whether that's true?
> 
> 
> And a separate, related question:
> 
> All I really want to get is the last-modified date for these records.
> 
> And it's kinda slow.
> 
> Using some code from the EUtilities_Web_Services HOWTO, I use the seq Fetch adaptor and the add_wanted_slot() Bio::Seq::SeqBuilder trick to get just the annotation part of a RichSeq object, and from there I pull out the dates using
> 
> $seq->annotation->get_Annotations('date_changed')
> 
> 
> Can someone suggest a faster way?
> 
> 
> Thanks,
> Dave
> 
> 
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