[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
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?
----- 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
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
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
Can someone suggest a faster way?
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