[Bioperl-l] Error retrieving sequence from BioSQL
Hilmar Lapp
hlapp at gmx.net
Fri Sep 29 21:30:29 UTC 2006
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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