[Bioperl-l] error running load_seqdatabase.pl

Thu Jan 12 22:27:00 EST 2006

Looks like the below modification Baohua Wang made to Root.pm works.  I did
run into another weird issue, but I think it is a sequence formatting
problem.  I try loading in a file with protein sequences in GenPept format
(pulled from BLASTP output using Bio::DB::GenPept and saved in a file using
SeqIO) after changing Root.pm:
______________________________________________________________________

C:\Perl\Scripts>load_seqdatabase.pl -dbname biosql -dbuser root -dbpass
****** -format genbank -safe NP_252217.gpt
Loading NP_252217.gpt ...

C:\Perl\Scripts>
______________________________________________________________________

Good!

The strangeness comes in when using Genpept seqs NOT passed through SeqIO
(pulled directly from NCBI, saved in a similar file).  Most sequences will
load, but a number of them will not:

______________________________________________________________________
C:\Perl\Scripts>load_seqdatabase.pl -dbname biosql -dbuser root -dbpass
crackers
ol -format genbank -safe NP_249092.gpt
Loading NP_249092.gpt ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values were
("","HAMAPMF_00220","0") FKs ()
Column 'dbname' cannot be null
---------------------------------------------------
Could not store Q59712:
------------- EXCEPTION  -------------
MSG: create: object (Bio::Annotation::DBLink) failed to insert or to be
found by
 unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:208
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
STACK Bio::DB::Persistent::PersistentObject::store
C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:272
STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
C:/Perl/site/lib/Bio\DB\BioSQL\AnnotationCollectionAdaptor.pm:219
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:216
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
STACK Bio::DB::Persistent::PersistentObject::store
C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:272
STACK Bio::DB::BioSQL::SeqAdaptor::store_children
C:/Perl/site/lib/Bio\DB\BioSQL\SeqAdaptor.pm:226
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:216
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
STACK Bio::DB::Persistent::PersistentObject::store
C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:272
STACK (eval) C:\Perl\Scripts\load_seqdatabase.pl:620
STACK toplevel C:\Perl\Scripts\load_seqdatabase.pl:603

--------------------------------------

 at C:\Perl\Scripts\load_seqdatabase.pl line 633

....

at C:\Perl\Scripts\load_seqdatabase.pl line 633
Could not store AAU82296:
------------- EXCEPTION  -------------
MSG: create: object (Bio::Species) failed to insert or to be found by unique
key

STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:208
STACK Bio::DB::Persistent::PersistentObject::create
C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:245
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:171
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
STACK Bio::DB::Persistent::PersistentObject::store
C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:272
STACK (eval) C:\Perl\Scripts\load_seqdatabase.pl:620
STACK toplevel C:\Perl\Scripts\load_seqdatabase.pl:603

--------------------------------------

 at C:\Perl\Scripts\load_seqdatabase.pl line 633
______________________________________________________________________

I'll check them out to try and derive what the differences are.  I will also
pass the above file through SeqIO to see what happens.  I think it could be
some of the GenPept formatted stuff is clogging up the works since I saved
everything in Genbank format through SeqIO.  For now, though, bioperl-db on
Windows works!  Any idea why the 'throw' change works?

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 
-----Original Message-----
From: drycafe at gmail.com [mailto:drycafe at gmail.com] On Behalf Of Hilmar Lapp
Sent: Wednesday, January 11, 2006 5:13 PM
To: Chris Fields; Steve Chervitz
Cc: bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] error running load_seqdatabase.pl

Interesting. That posting didn't receive much attention did it. So he
states:

<quote>
The script failed on throw() in loading Bio/Root/Root.pm on Windows.
The problem lines are those "throw $class (...".   After I put comma
after $class as "throw $class, (...", the BioSQL tests and load scripts
are succeeded
</quote>

Can anyone of those who wrote the Root exception and warning code
comment? Maybe Steve?

   -hilmar

On 1/11/06, Chris Fields <cjfields at uiuc.edu> wrote:
> Hilmar,
>
> As an update on what's going on:
>
> I've run into a few problems with load_seqdatabase.pl and bioperl-db on
> cygwin which I'll try to hash through this week; I'll post if I can't
figure
> it out soon.  It's not as buggy as trying to run it using the latest
> ActivePerl on WinXP, but it still has issues.
>
> I'm also looking through the ActiveState documentation for the latest
> version of perl they have (5.8.7), which I am running.  AFAIK, they enable
> dynamic loading when building.  I'll send them an email directly to see
what
> they say.  There may be some Win32-specific way of configuring a script
for
> dynamic loading of perl modules which isn't needed in other environments.
>
> There was also this previous email on bioperl-l:
>
> http://portal.open-bio.org/pipermail/bioperl-l/2005-May/018937.html
>
> Baohua Wang seemed to narrow it down somewhat, but I'm not sure if
changing
> the modules is a solution until I figure out why he made the changes.
They
> seem mainly geared towards getting load_seqdatabase to work with MsSQL,
but
> if he got it to work on Windows, then he may be onto something.  The
> modified Bio* modules can be found at:
>
> ftp://ftp.tc.cornell.edu/Outgoing/bwang/BioSQL-On-Windows
>
> I'll check them out to see if they work out and see what specific
> modifications he made (they're not detailed).
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Chris Fields
> Sent: Friday, January 06, 2006 1:28 PM
> To: 'Hilmar Lapp'
> Cc: bioperl-l at portal.open-bio.org
> Subject: RE: [Bioperl-l] error running load_seqdatabase.pl
>
> I'll try installing bioperl-db using Cygwin.  I know that I can connect to
> the native Windows mysql database from inside cygwin, so perhaps this will
> do as a short term workaround.  I'll also try using a different native
win32
> Perl version (maybe 5.6) and look into the dynamic loading issue.  I know
> that the AS Perl has given errors like this before and not had problems (I
> think it was also cranky with older versions bioperl), but this one is
> pretty serious.
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Friday, January 06, 2006 12:02 PM
> To: Chris Fields
> Cc: bioperl-l at portal.open-bio.org
> Subject: Re: [Bioperl-l] error running load_seqdatabase.pl
>
>
> On Jan 6, 2006, at 9:20 AM, Chris Fields wrote:
>
> > Hilmar,
> >
> > Did this ever get resolved?  I tried to reinstall a biosql database
> > using
> > bioperl-db and got the same problems.  I'll list out everything I ran
> > into
> > and what I pan on trying, as it's been a long time since I've tried
> > this.
> >
> > Currently, I'm using ActiveState Perl 5.8.7.813 on WinXP and MySQL
> > 4.1.14.
> > Using nmake and installing worked fine.  Loading the biosql schema and
> > loading taxonomy info also worked fine, although I had to manually
> > untar the
> > taxonomy archive so load_ncbi_taxonomy.pl could find the files (stupid
> > windows).  However, this is what happens when using
> > load_seqdatabase.pl:
> >
> > C:\Perl\Scripts>load_seqdatabase.pl -dbname dihydroorotase -dbuser root
> > NP_249092.gpt
> > Loading NP_249092.gpt ...
> > Undefined subroutine &Bio::Root::Root::debug called at
> > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1537,
> > <GEN0>
> > line 65.
> >
> > If I removed all args except the sequence file, it gives the same
> > response,
> > which means it happens before the connection is made to the database:
> >
>
> This happens indeed before a connection is made because it happens at
> the point it tries to dynamically load the BioSQL driver for the
> adaptor:
>
>         $self->debug("attempting to load driver for adaptor class
> $class\n");
>
> The BioSQL driver is loaded before the DBD driver is loaded.
>
> The module in which this happens (i.e., the persistence adaptor) has
> been loaded dynamically as well.
>
> Bio::Root::Root is in the 'use' statements, and the debug() method
> clearly exists. I'm at a loss as to why perl complains on certain
> Windows platforms. If somebody can tell me what, if anything, can be
> done to make this work on those platforms too I'll be glad to implement
> it.
>
> > [...]
> > Here's the error messages from that first test (warning it's very
> > messy):
> >
> > C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0,
> > 'bl
> > ib\lib', 'blib\arch')" t\01dbadaptor.t t\02species.t t\03simpleseq.t
> > t\04swiss.t t\05seqfeature.t t\06comment.t t\07dblink.t t\08genbank.t
> > t\09fuzzy2.t t\10ensembl.t t\11locuslink.t t\12ontology.t t\13remove.t
> > t\14query.t t\15cluster.t
> > t\01dbadaptor.....ok 1/19Subroutine new redefined at
> > [...]
> > Subroutine debug redefined at C:/Perl/site/lib/Bio\Root\Root.pm line
> > 356.
>
> So obviously it is there, right? So why doesn't perl see it a minute
> later?
>
> > [...]
> > I'll end with that.  At this moment, I can't see it working with the
> > current
> > setup.  I was using perl 5.8 with the old setup but I upgraded mysql
> > at some
> > point when working with gbrowse (I can't remember what the old version
> > was);
> > I'll try upgrading to the newest ActiveState version to see what
> > happens.
> > Could it be the MySQL version?
>
> I don't think it has anything to do with the MySQL version, or the DBD
> driver for that matter. Instead, it looks like on issue with dynamic
> loading of perl modules on your particular platform.
>
>         -hilmar
>
> >
> > Christopher Fields
> > Postdoctoral Researcher - Switzer Lab
> > Dept. of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>

--
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: Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
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