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

Mark A. Jensen maj at fortinbras.us
Tue Apr 20 21:30:11 EDT 2010


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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