[Bioperl-l] EUtilities overhaul started

Chris Fields cjfields at uiuc.edu
Sat Jun 2 10:39:25 EDT 2007


Yes, there are a few odd issues, though that's one I've not heard of  
yet.  You might try one of the sub-nucleotide databases (nuccore,  
nucest, nucgss).

I'll try looking into it and (if necessary) pester NCBI about it.   
I'll pass this on to the mail list to see if anyone else knows about  
the problem.

chris

On Jun 2, 2007, at 8:28 AM, Bernd Brandt wrote:

> Hi Chris,
>
> Thanks for your work on EUtilities.
> For a production task, I used EUtilitities directly (given your
> announced overhaul). I noticed a recent problem at NCBI (reported two
> weeks ago to NCBI, no reply yet). Possibly you may run into this with
> testing: if you ePOST gi ids to the EU server and then use this set in
> Esearch (using the query key) no results are returned for the
> nucleotide database.
> ESearches like "db=$db%23$QueryKey" typically fail if the $db is
> nucleotide (but work f $db='protein'). The XML output has Count 0 and
> an empty QueryTranslationSet for db=nucleotide only.
> For completeness, I attach a simple test script I used.
>
>
> Best regards,
> Bernd
>
>
> On 6/2/07, Chris Fields <cjfields at uiuc.edu> wrote:
>> To anyone using Bio::DB::EUilities,
>>
>> I am in the midst of a major overhaul to the various EUtilities tools
>> and to Bio::DB::GenericWebDBI (the latter which I am forming into
>> more or less a test bed for other database interfaces).  I'm about
>> 80% done at this point, and will likely start committing changes this
>> coming week.
>>
>> The overall interface will change (something I had warned about in
>> the Bio::DB::EUtilities POD) but I am hoping it will be more
>> intuitive and easier to use in the long run.  I'll describe the
>> overall redesign and use in an upcoming HOWTO (as recommended by
>> Brian a while back).
>>
>> If anyone has any suggestions/ideas/flames, please let me know!
>>
>> Cheers!
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> <EUsearch.pl>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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