[Bioperl-l] Eutilities epost/efetch problem
cjfields at illinois.edu
Tue May 12 14:57:32 EDT 2009
Same here (no error). Just ran the below.
my @gi_number = qw(
my $gpeptfactory = Bio::DB::EUtilities->new(
-eutil => 'epost',
-db => 'protein',
-rettype => 'gp',
-retmode => 'text',
-tool => 'VKCDB_Update',
-email => 'wgallin at ualberta.ca',
-id => \@gi_number,
-keep_histories => 1);
my $hist = $gpeptfactory->next_cookie || die "Arghh!";
$gpeptfactory->set_parameters(-eutil => 'efetch',
-history => $hist);
$gpeptfactory->get_Response(-file => '>test.gb');
On May 12, 2009, at 1:42 PM, Kristine Briedis wrote:
> Hi Chris,
> I'm not getting the error anymore. NCBI must have fixed something.
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at illinois.edu]
> Sent: Tuesday, May 12, 2009 11:36 AM
> To: Kristine Briedis
> Cc: Warren Gallin; BioPerl List
> Subject: Re: [Bioperl-l] Eutilities epost/efetch problem
> Not showing up in tests, so this may be something very specific that
> changed. I'll try to reproduce it.
> On May 12, 2009, at 12:19 PM, Kristine Briedis wrote:
>> Hi Warren,
>> We've noticed the same EFetch error. I emailed NCBI and will let
>> you know what they say.
>> Kristine Briedis, Ph.D.
>> Bioinformatics Software Engineer
>> Accelrys, Inc.
>> 10188 Telesis Court, Suite 100
>> San Diego, CA 92121 USA
>> kbriedis at accelrys.com
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org
>> ] On Behalf Of Warren Gallin
>> Sent: Monday, May 11, 2009 6:36 PM
>> To: BioPerl List
>> Subject: [Bioperl-l] Eutilities epost/efetch problem
>> Hi folks,
>> Something started failing for me this morning that had been working
>> reliably for the last week,
>> I post an array of gi numbers, a history is successfully returned,
>> but when I try to use efetch to get the records, it fails with the
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Response Error
>> Not Found
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /Library/Perl/5.8.8/Bio/Root/Root.pm:
>> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.8/
>> STACK: 090507_Stable_gb_update.pl:238
>> I'm running the efetch inside an eval and letting it try a total
>> of 6
>> times with a 5 sedond sleep in between, but the error is consistent.
>> So I consider two possibilities:
>> 1) Has something changed on the Entrez server recently? Has anyone
>> else started having this kind of problem?
>> 2) Have I inserted some subtle flaw into my code that would lead
>> to a
>> failure of efetch.
>> I am attaching two text files, one with the code chunklet that is
>> doing this and the other the output from the script.
>> Any help or suggestions are profoundly appreciated.
>> Warren Gallin
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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