[Gmod-help] gmod_bulk_load_gff3.pl
Scott Cain
cain.cshl at gmail.com
Fri Feb 29 09:09:19 EST 2008
Hi Todd,
I'm trying to catch up on my email after being gone for a few days--did
you get this resolved?
Scott
On Fri, 2008-02-22 at 13:01 -0500, todd.moughamer at syngenta.com wrote:
> Scott,
>
> The BioPerl live updated fixed the "Can't locate object method
> "database" problem (Thanks!). The loading progresses much further but
> now errors out with the message below. Here I am using the first 100
> lines of the sample yeast GFF file which did not produce errors in the
> GFF3 validator:
>
> Preparing data for inserting into the chadotest database
> (This may take a while ...)
> Loading data into feature table ...
> Loading data into featureloc table ...
> Skipping feature_relationship table since the load file is empty...
> Loading data into featureprop table ...
> DBD::Pg::db pg_endcopy failed: ERROR: invalid input syntax for integer:
> ""
> CONTEXT: COPY featureprop, line 1, column type_id: ""
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: calling endcopy for featureprop failed:
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
> STACK: Bio::GMOD::DB::Adapter::copy_from_stdin
> /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:2723
> STACK: Bio::GMOD::DB::Adapter::load_data
> /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:2644
> STACK: /usr/bin/gmod_bulk_load_gff3.pl:912
> -----------------------------------------------------------
> Issuing rollback() for database handle being DESTROY'd without explicit
> disconnect().
>
> Thanks,
>
> Todd
>
> -----Original Message-----
> From: Scott Cain [mailto:cain.cshl at gmail.com]
> Sent: Wednesday, February 20, 2008 11:45 AM
> To: Moughamer Todd USRE
> Cc: hlapp at duke.edu; help at gmod.org
> Subject: RE: [Gmod-help] gmod_bulk_load_gff3.pl
>
> Hi Todd,
>
> The ##gff-version error it reported won't be a problem; the loader is
> quite forgiving about that. The invalid type problems could potentially
> be a problem though. Here's the thing: Chado uses SO (so yes, you
> should be using so.obo) for feature types, while the current GFF3 spec
> requires SOFA (I've been advocating for changing the spec and it
> probably will change in the near future).
>
> So, if the validator is complaining about those terms because they
> aren't in SOFA, but they are in SO, that's no problem. But if they
> aren't in SO either (if, for instance, they've been obsoleted), then
> you'll have to fix the file. When I confronted with something like
> that, I just do a global search and replace on the term to swap in the
> nearest term in SO.
>
> Scott
>
> On Wed, 2008-02-20 at 11:34 -0500, todd.moughamer at syngenta.com wrote:
> > Hi Scott,
> >
> > We downloaded Chado from CVS. We are in the process of installing the
> > live BioPerl.
> >
> > I am using the example yeast GFF3 files from the web site
> > (http://www.gmod.org/wiki/index.php/Load_GFF_Into_Chado). I ran them
> > through the validator and sure enough they came back invalid (both the
>
> > original and sorted forms). Here are some some of the errors:
> >
> > Line Number Error/Warning
> > ----------- -------------
> > 1 [ERROR] first line must be ##gff-version 3 (line: SGD)
> > 350 [ERROR] invalid type (type: gene_cassette)
> > 352 [ERROR] invalid type (type: gene_cassette)
> > 369 [ERROR] invalid type (type: gene_cassette)
> > 1065 [ERROR] invalid type (type: long_terminal_repeat)
> > 1066 [ERROR] invalid type (type: long_terminal_repeat)
> > 1072 [ERROR] invalid type (type: transposable_element_gene)
> > ...
> >
> > I'm also wondering if I should be using the sofa.obo file rather than
> > the so.obo file I downloaded from sequenceontology.org?
> >
> > Thanks,
> >
> > Todd
> >
> > -----Original Message-----
> > From: Scott Cain [mailto:cain.cshl at gmail.com]
> > Sent: Tuesday, February 19, 2008 3:49 PM
> > To: Hilmar Lapp
> > Cc: Moughamer Todd USRE; help at gmod.org
> > Subject: Re: [Gmod-help] gmod_bulk_load_gff3.pl
> >
> > OK, after running some tests, I still think an out of date BioPerl is
> > probably at fault. With a current checkout of both the schema and
> > bioperl repositories, I can load GFF3 data with Dbxref tags
> > successfully.
> >
> > Todd, a few questions for you:
> >
> > * are you using a cvs checkout of chado as well? I should have asked
> > that before telling you to update bioperl.
> >
> > * If you are using current checkouts of chado and bioperl and still
> > have the problem, could you please run your GFF3 through the GFF3
> > validator to see if it turns up any problems:
> >
> > http://dev.wormbase.org/db/validate_gff3/validate_gff3_online
> >
> > * If you still get the same error message, could you please send me a
> > sample of the offending GFF3? There may be a case that I didn't think
>
> > of.
> >
> > Thanks,
> > Scott
> >
> > On Tue, 2008-02-19 at 14:13 -0500, Scott Cain wrote:
> > > Hi Hilmar,
> > >
> > > Hah! I was getting ready to write a response where I basically said
>
> > > I
> >
> > > didn't think that was what was going on, and I would have justified
> > > it
> >
> > > with some hand waving, since I didn't have the actual error message,
>
> > > so I was just guessing and hopefully, updating bioperl will fix the
> > > problem (and that still is a possibility).
> > >
> > > However, I do have the actual error message, so I went and looked
> > > the offending line, and it is in a method called 'handle_dbxref', so
>
> > > it looks like your diagnosis is spot on. Now I need to figure out
> > > if this is still happening with bioperl-live and figure out why.
> > > I've got a
> > > Bio::SeqFeature::Annotated->annotation->get_Annotations('Dbxref'),
> > which I think should return a list of DBLink features. I guess I'll
> > go see.
> > >
> > > Thanks for pointing that out!
> > > Scott
> > >
> > > On Tue, 2008-02-19 at 13:55 -0500, Hilmar Lapp wrote:
> > > > Well, B::A::SimpleValue never had a method called database(). It
> > > > is B::A::DBLink that has that (and always had).
> > > >
> > > > So my first diagnosis from afar would be that something is
> > > > returning
> >
> > > > or creating a B::A::SimpleValue when it was expected to return or
> > > > create a B::A::DBLink.
> > > >
> > > > -hilmar
> > > >
> > > > On Feb 19, 2008, at 1:07 PM, Scott Cain wrote:
> > > >
> > > > > Hi Todd,
> > > > >
> > > > > Yes, that is still the most likely solution for you. A few
> > > > > months
> >
> > > > > ago, the BioPerl API changed and Bio::Annotation::SimpleValue
> > > > > objects don't work the same way that they used to, thus the
> > > > > error you are seeing.
> > > > > It's not really looking for a method named 'database'; that is
> > > > > an artifact left over from the API change.
> > > > >
> > > > > Scott
> > > > >
> > > > > On Tue, 2008-02-19 at 11:59 -0500, todd.moughamer at syngenta.com
> > wrote:
> > > > >> I run into the following error when trying to load Chado:
> > > > >>
> > > > >> gmod_bulk_load_gff3.pl --organism yeast --gfffile
> > > > >> ~/tmp/saccharomyces_cerevisiae.gff.sorted --dbname chadotest
> > > > >> Preparing data for inserting into the chadotest database (This
> > > > >> may take a while ...) Can't locate object method "database" via
>
> > > > >> package "Bio::Annotation::SimpleValue"
> > > > >> at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line
> > > > >> 3061, <GEN0> line 1.
> > > > >> Issuing rollback() for database handle being DESTROY'd without
> > > > >> explicit disconnect().
> > > > >>
> > > > >> I found reference to this problem online
> > > > >> (http://www.nabble.com/question-about-gmod_bulk_load_gff3.pl-
> > > > >> td15135949.html) with the recommendation of downloading the
> > 'live'
> > > > >> version of BioPerl. However, upon browsing the latest code in
> > > > >> SVN
> >
> > > > >> I do not see inclusion of a "database" method. Is this still
> > > > >> the recommended solution to the problem?
> > > > >>
> > > > >> Thanks,
> > > > >>
> > > > >> Todd
> > > > >>
> > > > >>
> > > > >> Todd Moughamer
> > > > >>
> > > > >> Bioinformatics Consultancy & Training Group
> > > > >>
> > > > >> Syngenta Biotechnology, Inc.
> > > > >>
> > > > >> 3054 Cornwallis Road, 1243.E
> > > > >>
> > > > >> Research Triangle Park, NC 27709-2257
> > > > >>
> > > > >> Tel: 919-597-3078
> > > > >>
> > > > >> Email: todd.moughamer at syngenta.com www.syngenta.com
> > > > >>
> > > > >>
> > > > > --
> > > > >
> > ----------------------------------------------------------------------
> > > > > --
> > > > > Scott Cain, Ph. D.
> > > > > cain at cshl.edu
> > > > > GMOD Coordinator (http://www.gmod.org/)
> > > > > 216-392-3087
> > > > > Cold Spring Harbor Laboratory
> > > > >
> > > >
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. cain.cshl at gmail.com
> GMOD Coordinator (http://www.gmod.org/) 216-392-3087
> Cold Spring Harbor Laboratory
>
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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