[Bioperl-l] Error retrieving sequence from BioSQL

Brian Osborne osborne1 at optonline.net
Sat Sep 30 18:03:49 EDT 2006


Seth,

All these tests are passing for me with the latest bioperl-live and
bioperl-db.

Brian O.


On 9/30/06 5:44 PM, "Seth Johnson" <johnson.biotech at gmail.com> 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 :
>> ===========================================================
>> 
>> 
>> 
>> 
>> 
>> 
> 




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