[Bioperl-l] EUtilities overhaul started

Chris Fields cjfields at uiuc.edu
Sun Jun 3 00:51:57 EDT 2007


I can confirm this; however it only relates to the use of history  
with esearch and nucleotide (use of the history with other eutils  
seems to work fine); retrieving sequences via efetch is not  
affected.  If I find out anything more I'll post something on the  
mail list.

chris

On Jun 2, 2007, at 11:48 AM, Bernd Brandt wrote:

> I can confirm that using the correct sub-nucleotide database works
> (nuccore in my case).
> This seems to be a quite recent change/bug at NCBI. Until recently,
> db=nucleotide worked. Moreover, EInfo still lists nucleotide as valid
> db.
> It is not optimal to have to choose the sub-database and the searches
> work via the Entrez web-interface. Note that this problem is related
> to the ESearch and db=nucleotide.
>
> bernd
>
> On 6/2/07, Chris Fields <cjfields at uiuc.edu> wrote:
>> 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
>>
>>
>>
>>

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





More information about the Bioperl-l mailing list