[Bioperl-l] Error retrieving sequence from BioSQL

Seth Johnson johnson.biotech at gmail.com
Sat Sep 30 19:10:11 EDT 2006


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


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