[Bioperl-l] Error retrieving sequence from BioSQL

Hilmar Lapp hlapp at gmx.net
Sat Sep 30 18:02:41 EDT 2006


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 :
===========================================================







More information about the Bioperl-l mailing list