[Bioperl-l] Error retrieving sequence from BioSQL

Seth Johnson johnson.biotech at gmail.com
Sat Sep 30 17:44:24 EDT 2006


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


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