[Bioperl-l] Error retrieving sequence from BioSQL

Chris Fields cjfields at uiuc.edu
Sat Sep 30 18:28:08 EDT 2006


I'll try to run some additional tests on WinXP to confirm this, but  
it won't be until tomorrow.  I don't see this on Mac OS X, though.

My recollection was that I needed to run 'nmake install' before  
running 'nmake test' to get tests to work properly on WinXP, but I  
haven't done it in a while.

Chris

On Sep 30, 2006, at 5:02 PM, Hilmar Lapp wrote:

> It doesn't shed more light but it does raise an alert flag. All tests
> are supposed to pass. The fact that they don't means the problems you
> are seeing have nothing to do with your specific data or script.
>
> First off - can anyone else confirm those errors using the latest
> Bioperl-db and Bioperl?
>
> Second - Seth could you run those tests individually, e.g., using
>
> 	$ make test test_02species TEST_VERBOSE=1
>
> and similarly for the other tests that have failures and post the
> output. Let's start with 02species and 03simpleseq.
>
> 	-hilmar
>
> On Sep 30, 2006, at 5:44 PM, Seth Johnson wrote:
>
>> There are errors during the test. Here's their summary:
>> ____________________________
>> Failed Test     Stat Wstat Total Fail  Failed  List of Failed
>> -------------------------------------------------------------
>> t\02species.t                 65    2   3.08%  63 65
>> t\03simpleseq.t    1   256    59  106 179.66%  7-59
>> t\04swiss.t                   52   14  26.92%  25 27-34 38-42
>> t\12ontology.t     2   512   738 1471 199.32%  3-738
>> t\16obda.t                    12    3  25.00%  10-12
>> ____________________________
>>
>> May be that can shed some light on the problem?!?!
>>
>> On 9/29/06, Hilmar Lapp < hlapp at gmx.net> wrote:This may in fact be
>> a knock-on effect of the fixes? <sigh>
>>
>> Seth, did you run the test suite that comes with bioperl-db, and did
>> you get any errors?
>>
>>         -hilmar
>>
>> On Sep 28, 2006, at 2:26 PM, Chris Fields wrote:
>>
>>> Seth,
>>>
>>> The organism issue is a bug and has been reported, though I thought
>>> it was fixed.
>>>
>>> The lack of the date and the version is a bit odd, but there have
>>> been a lot of changes lately to bioperl-live (core bioperl in CVS),
>>> and a few to bioperl-db.  How old is your bioperl and bioperl-db
>>> installation.  Hilmar, any additional thoughts?
>>>
>>> Chris
>>>
>>> On Sep 28, 2006, at 11:10 AM, Seth Johnson wrote:
>>>
>>>> Thank you.  That takes care of that, however, I do have another
>>>> gripe.  When
>>>> running my script, quoted before, with "my $out =
>>>> Bio::SeqIO->newFh('-format' => 'genbank');", I have several key
>>>> pieces of
>>>> information missing.  The most important one is the version
>>>> number.  There's
>>>> also a date missing, and source organism name is corrupted.
>>>> Here's what I
>>>> get:
>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>>> LOCUS       NM_014580               2145 bp    dna     linear   UNK
>>>> DEFINITION  Homo sapiens solute carrier family 2, (facilitated
>>>> glucose
>>>>             transporter) member 8 (SLC2A8), mRNA.
>>>> ACCESSION   NM_014580
>>>> SOURCE      sapiens.
>>>>   ORGANISM  sapiens
>>>>             Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa;
>>>> Bilateria;
>>>>             Coelomata; Deuterostomia; Chordata; Craniata;
>> Vertebrata;
>>>>             Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii;
>>>> Tetrapoda;
>>>>             Amniota; Mammalia; Theria; Eutheria; Euarchontoglires;
>>>> Primates;
>>>>             Haplorrhini; Simiiformes; Catarrhini; Hominoidea;
>>>> Hominidae;
>>>>             Homo/Pan/Gorilla group; Homo.
>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>>>
>>>> All of the missing information is stored in BioSQL and
>>>> theoretically should
>>>> be in the outpu. Here's how NCBI genbank file looks:
>>>>
>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>>>
>>>> LOCUS       NM_014580               2145 bp    mRNA    linear
>>>> PRI 17-OCT-2005
>>>> DEFINITION  Homo sapiens solute carrier family 2, (facilitated
>>>> glucose
>>>>             transporter) member 8 (SLC2A8), mRNA.
>>>> ACCESSION   NM_014580
>>>> VERSION     NM_014580.3  GI:51870928
>>>> KEYWORDS    .
>>>> SOURCE      Homo sapiens (human)
>>>>   ORGANISM  Homo sapiens
>>>> <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606 >
>>>>             Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
>>>> Euteleostomi;
>>>>             Mammalia; Eutheria; Euarchontoglires; Primates;
>>>> Haplorrhini;
>>>>             Catarrhini; Hominidae; Homo.
>>>>
>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>>>
>>>>
>>>> On 9/28/06, Chris Fields <cjfields at uiuc.edu> wrote:
>>>>>
>>>>> Those are from the excessively paranoid '-w' flag on the shebang
>>>>> line.  If you remove the flag but add the 'use warnings' pragma
>> the
>>>>> 'subroutine x redefined' warnings go away.  This, BTW, is one
>> of the
>>>>> quirks of the ActivePerl distribution; other OSs don't have the
>> same
>>>>> problem.
>>>>>
>>>>> The 'solution' described on that page is actually a workaround,
>>>>> not a
>>>>> bugfix.  It causes problems with stack traces with error handling
>>>>> but
>>>>> seems harmless beyond that.  I haven't been able to find a
>>>>> satisfactory fix which works on all OS's.
>>>>>
>>>>> Chris
>>>>>
>>>>>
>>>>> On Sep 28, 2006, at 10:42 AM, Seth Johnson wrote:
>>>>>
>>>>>> This is under Windows, but using ActiveState Komodo 3.5 and their
>>>>>> latest Perl for Windows and latest BioPerl & BioPerl-db from CVS.
>>>>>>
>>>>>> I actually just stumbled upon a solution.  It's described in the
>>>>>> "Installing Bioperl on Windows" by adding a comma after
>> $class: in
>>>>>> Bio::Root::Root throw() subroutine.  Thanks for hinting me about
>>>>>> what I run it on.
>>>>>>
>>>>>> The code works now, BUT it spews whole bunch of warnings about
>>>>>> "Subroutine .... redefined":
>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>> Subroutine new redefined at c:/Perl/site/lib/Bio\BioEntry
>>>>>> .pm line 88.
>>>>>> Subroutine object_id redefined at c:/Perl/site/lib/Bio
>> \BioEntry.pm
>>>>>> line 128.
>>>>>> Subroutine version redefined at c:/Perl/site/lib/Bio\BioEntry.pm
>>>>>> line 150.
>>>>>> Subroutine authority redefined at c:/Perl/site/lib/Bio
>> \BioEntry.pm
>>>>>> line 171.
>>>>>> Subroutine namespace redefined at c:/Perl/site/lib/Bio
>> \BioEntry.pm
>>>>>> line 192.
>>>>>> Subroutine display_name redefined at c:/Perl/site/lib/Bio
>>>>>> \BioEntry.pm line 217.
>>>>>> Subroutine description redefined at c:/Perl/site/lib/Bio
>>>>>> \BioEntry.pm line 241.
>>>>>> Subroutine new redefined at c:/Perl/site/lib/Bio\Root\Root.pm
>> line
>>>>>> 201.
>>>>>> Subroutine verbose redefined at c:/Perl/site/lib/Bio\Root\Root.pm
>>>>>> line 234.
>>>>>> Subroutine _register_for_cleanup redefined at c:/Perl/site/lib/
>> Bio
>>>>>> \Root\Root.pm line 246.
>>>>>> Subroutine _unregister_for_cleanup redefined at c:/Perl/site/lib/
>>>>>> Bio
>>>>>> \Root\Root.pm line 256.
>>>>>> Subroutine _cleanup_methods redefined at c:/Perl/site/lib/Bio
>> \Root
>>>>>> \Root.pm line 263.
>>>>>> Subroutine throw redefined at c:/Perl/site/lib/Bio\Root\Root.pm
>>>>>> line 316.
>>>>>> Subroutine debug redefined at c:/Perl/site/lib/Bio\Root\Root.pm
>>>>>> line 379.
>>>>>> Subroutine _load_module redefined at c:/Perl/site/lib/Bio\Root
>>>>>> \Root.pm line 398.
>>>>>> Subroutine DESTROY redefined at c:/Perl/site/lib/Bio\Root\Root.pm
>>>>>> line 426.
>>>>>> Subroutine new redefined at c:/Perl/site/lib/Bio\Root\RootI.pm
>> line
>>>>>> 117.
>>>>>> Subroutine _initialize redefined at c:/Perl/site/lib/Bio\Root
>>>>>> \RootI.pm line 128.
>>>>>> ...
>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>>
>>>>>>
>>>>>> On 9/28/06, Chris Fields <cjfields at uiuc.edu> wrote: I had
>> problems
>>>>>> with bioperl-db on native WinXP (not cygwin), but I
>>>>>> did manage to get it running in cygwin with some effort.  The
>> issue
>>>>>> on native WinXP was related to Bio::Root::Root::throw(), though.
>>>>>>
>>>>>> There is a bug and workaround filed on Bugzilla, but I haven't
>>>>>> worked
>>>>>> on it in a while (and the workaround has some problems as
>> well).  I
>>>>>> may try running it again to see what happens.
>>>>>>
>>>>>> http://bugzilla.open-bio.org/show_bug.cgi?id=1938
>>>>>>
>>>>>> Chris
>>>>>>
>>>>>> On Sep 28, 2006, at 9:04 AM, Hilmar Lapp wrote:
>>>>>>
>>>>>>> Very odd. This is under Windows, presumably using Cygwin?
>>>>>>>
>>>>>>> The method Bio::Root::Root::throw() clearly exists, and
>>>>>>> PersistentObject inherits from it. The exception it was
>> trying to
>>>>>>> throw has nothing to do with failure or success to find the
>>>>>>> database
>>>>>>> row (actually it did succeed since otherwise it wouldn't
>> construct
>>>>>>> the object) but with dynamically loading a class, presumably
>>>>>>> Bio::DB::Persistent::Seq.
>>>>>>>
>>>>>>> Are you using the 1.5.x release of bioperl?
>>>>>>>
>>>>>>> Does anyone on the list have any experience with these sorts of
>>>>>>> things on Windows?
>>>>>>>
>>>>>>> (Seth, I've moved this thread to the bioperl list, since this is
>>>>>> what
>>>>>>> the problem is about.)
>>>>>>>
>>>>>>>       -hilmar
>>>>>>>
>>>>>>> On Sep 27, 2006, at 1:39 PM, Seth Johnson wrote:
>>>>>>>
>>>>>>>> Hello guys,
>>>>>>>>
>>>>>>>> I successfully populated the biosql database, thanks to you.
>>>>>>>> Now,
>>>>>>>> I'm
>>>>>>>> trying to retrieve a sequence from it following the example
>> from
>>>>>>>> BOSC2003
>>>>>>>> slides and ran into uninformative error (at least to me it
>>>>>>>> doesn't
>>>>>>>> mean
>>>>>>>> anyting).  I suspect that I'm missing something and hope you
>> can
>>>>>>>> point me in
>>>>>>>> the right direction.  Here's my source code:
>>>>>>>>
>>>>>>
>> -------------------------------------------------------------------
>>>>>> --
>>>>>>>> -
>>>>>>>> ---
>>>>>>>> #!/usr/bin/perl -w
>>>>>>>> use strict;
>>>>>>>> use warnings;
>>>>>>>>
>>>>>>>> use Bio::Seq;
>>>>>>>> use Bio::Seq::SeqFactory;
>>>>>>>> use Bio::DB::SimpleDBContext;
>>>>>>>> use Bio::DB::BioDB;
>>>>>>>>
>>>>>>>> my $dbc = Bio::DB::SimpleDBContext->new(
>>>>>>>>     -driver => 'mysql',
>>>>>>>>     -dbname => 'BioSQL_1',
>>>>>>>>     -host => ' 192.168.1.3',
>>>>>>>>     -user => 'xxxxx',
>>>>>>>>     -pass => 'xxxxxx'
>>>>>>>> );
>>>>>>>>
>>>>>>>> my $db = Bio::DB::BioDB->new(-database  => 'biosql',
>>>>>>>>                             -dbcontext => $dbc);
>>>>>>>>
>>>>>>>> my $seq = Bio::Seq->new(-accession_number => 'NM_014580', -
>>>>>>>> namespace =>
>>>>>>>> 'refseq_H_sapiens');
>>>>>>>> my $seqfact = Bio::Seq::SeqFactory->new(-type => 'Bio::Seq');
>>>>>>>> my $adp = $db->get_object_adaptor($seq);
>>>>>>>> my $dbseq = $adp->find_by_unique_key($seq, -obj_factory =>
>>>>>> $seqfact);
>>>>>>>>
>>>>>>>> my $out = Bio::SeqIO->newFh('-format' => 'EMBL');
>>>>>>>> print $out $dbseq;
>>>>>>>>
>>>>>>>> exit;
>>>>>>>>
>> -----------------------------------------------------------------
>>>>>>>>
>>>>>>>> Just when the "find_by_unique_key" function is executed I
>> get the
>>>>>>>> following
>>>>>>>> error:
>>>>>>>>
>>>>>>>> ================================
>>>>>>>> Undefined subroutine &Bio::Root::Root::throw called at
>>>>>>>> c:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm line
>> 199.
>>>>>>>> ================================
>>>>>>>>
>>>>>>>> The sequence does exist in the database. I checked that.  Any
>>>>>>>> ideas???
>>>>>>>>
>>>>>>>> --
>>>>>>>> Best Regards,
>>>>>>>>
>>>>>>>>
>>>>>>>> Seth Johnson
>>>>>>>> Senior Bioinformatics Associate
>>>>>>>> _______________________________________________
>>>>>>>> BioSQL-l mailing list
>>>>>>>> BioSQL-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Best Regards,
>>>>>>
>>>>>>
>>>>>> Seth Johnson
>>>>>> Senior Bioinformatics Associate
>>>>>>
>>>>>> Ph: (202) 470-0900
>>>>>> Fx: (775) 251-0358
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Best Regards,
>>>>
>>>>
>>>> Seth Johnson
>>>> Senior Bioinformatics Associate
>>>>
>>>> Ph: (202) 470-0900
>>>> Fx: (775) 251-0358
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>>
>>
>>
>> -- 
>> Best Regards,
>>
>>
>> Seth Johnson
>> Senior Bioinformatics Associate
>>
>> Ph: (202) 470-0900
>> Fx: (775) 251-0358
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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





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