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

Mark A. Jensen maj at fortinbras.us
Wed Apr 21 00:13:05 EDT 2010


As I remember, the two were slightly different, but only at the most aggravating 
points. The parameters don't map completely consistently; I think there is a 
kludge or two in SoapEU that makes sure certain things work (like taking -retmax 
to -RetMax, 'cause all of sudden there's case sensitivity). I wasn't very 
systematic about this, however-- One aggravating thing was the 'unspecified 
internal error' (or was it the 'lazy contractor error'?), that seems to get 
thrown when you specify a general parameter (like retmax) that doesn't happen to 
be used by the method you're calling. Seems to me that these were just ignored 
under original EU. And so on.-- MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Dave Messina" <David.Messina at sbc.su.se>; "BioPerl List" 
<bioperl-l at lists.open-bio.org>
Sent: Tuesday, April 20, 2010 11:32 PM
Subject: Re: [Bioperl-l] NCBI efetch: request limits and getting dates fast


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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