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

Dave Messina David.Messina at sbc.su.se
Tue Apr 20 13:22:39 EDT 2010


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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