[Gmod-help] GFF loading script

[Scott Cain]

Hi Dave,

I answered this yesterday but forgot to "reply all" ( hey it happens
to all of us occasionally).

Scott

On Thursday, June 18, 2009, Yap, Soon <syap at jcvi.org> wrote:
> Hi Scott,
>
>   Sorry for my own mistake, apparently I missed out the Module::Load from perl. I just change the library and it pointed to the wrong one. After I've recompile everything, and it's working fine now. I'm able to load the database and able to use Artemis to view the annotation.
>
>   Thank you very much for your guidance!
>
>   Thanks and regards,
>
> SoonJoo
>
> -----Original Message-----
> From: Scott Cain [mailto:scott at scottcain.net]
> Sent: Thursday, June 18, 2009 1:22 PM
> To: Yap, Soon
> Subject: Re: [Gmod-help] GFF loading script
>
> Hello SoonJoo,
>
> What version of Chado are you using?  As far as I can recall, the bulk
> loader never used Bio::GMOD::Load (for that matter, I don't think any
> loader ever used Bio::GMOD::Load--I started writing it and abandoned
> it for another approach).  Or, are you sure your using
> gmod_bulk_load_gff3.pl?
>
> Another issue that is much less important is that you shouldn't need
> to sort the saccharomyces_cerevisiae gff3 file--it is already sorted
> when you get it from yeastgenome.org <http://yeastgenome.org>.  Generally, if a GFF3 file
> doesn't need sorting, I don't do it, since it means related features
> will typically have contigous feature_ids.  Of course this doesn't
> matter for the functioning of the database, but if you ever what to
> find things by query on the command line, it can make that a little
> easier.
>
> Scott
>
>
> On Thu, Jun 18, 2009 at 12:14 AM, Yap, Soon<syap at jcvi.org> wrote:
>> Hi,
>>
>> I've try to load the sample GFF file to my database (running
>> gmod_bulk_load_gff3.pl --organism yeast  --gfffile
>> /home/soonjoo/Desktop/saccharomyces_cerevisiae.sorted.gff ). But I'm facing
>> a problem with the following error message.
>>
>> DBD::Pg::st execute failed: ERROR:  more than one row returned by a subquery
>> used as an expression [for Statement "SELECT indkey FROM pg_catalog.pg_index
>> WHERE indisprimary=true AND indrelid=(
>> SELECT oid FROM pg_catalog.pg_class
>> WHERE relname = ?)
>> " with ParamValues: 1='genotype'] at
>> /usr/local/lib/perl5/site_perl/5.10.0/DBIx/ContextualFetch.pm line 52.
>> Compilation failed in require at
>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/GMOD/Load.pm line 3.
>> BEGIN failed--compilation aborted at
>> /usr/local/lib/perl5/site_perl/5.10.0/Bio/GMOD/Load.pm line 3.
>>
>> I can't figure out what is the problem with the script. Any help would be
>> really appreciated.
>>
>> Thanks and regards
>>
>> SoonJoo,Yap
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research