[Bioperl-l] Error retrieving sequence from BioSQL

Chris Fields cjfields at uiuc.edu
Sun Oct 1 13:17:24 EDT 2006


The '-w' flag on the shebang line is the source of those errors.  I  
never set it anymore on Windows due to this; I just use the 'use  
warnings' pragma.

If you use 'perl -I. t/test.t' you can normally get around the '-w'  
assumed by using 'make test'.

I will try running tests on bioperl-db and bioperl tomorrow on WinXP  
to confirm these.

Chris

On Sep 30, 2006, at 6:10 PM, Seth Johnson wrote:

> How do I get rid of all of the warnings for "redefined subroutines"  
> during
> the test??  It clutters the output and I can't see the errors.
>
> On 9/30/06, Hilmar Lapp <hlapp at gmx.net> 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 :
>> ===========================================================
>>
>>
>>
>>
>>
>>
>
>
> -- 
> 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





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