Re: Error in gmod_bulk_load_gff3.pl

Sure, a small sample is attached.  I hadn't made the connection that
Bio::Annotation::Target related to one of the gff attributes, never
used GMOD perl/ BioPerl before.

Thanks for looking into this!
Richard.

Scott Cain wrote:
> Hi Richard,
> 
> I just tried installing yeast data into a fresh chado instance and it
> worked fine, but it didn't have any features that used the Target
> attribute (which is what seems to be giving you a problem).  Could you
> send me a sample of your data?
> 
> Thanks,
> Scott
> 
> 
> On Tue, Feb 10, 2009 at 9:09 AM, Scott Cain <scott <at> scottcain.net> wrote:
>> Hi Richard,
>>
>> That is a bioperl problem.  I haven't tried the official 1.6 release
>> with chado, but it was working from cvs not that long ago.  I'll do
>> some testing with the official release and get back to you.
>>
>> Scott
>>
>>
>> On Tue, Feb 10, 2009 at 8:08 AM, Richard Smith <richard <at> flymine.org> wrote:
>>> Hi all,
>>> I am trying to load some gff files into a new chado database using
>>> gmod_bulk_load_gff3.pl and have got an error.
>>>
>>> I downloaded gmod-1.0 and followed the INSTALL.Chado instructions - this
>>> was a clean install on mac OS X Leopard, I installed the latest versions
>>> of all required perl modules from CPAN.
>>>
>>> Setting up the chado database and loading up the sequence ontology, etc
>>> was fine.  Running:
>>>
>>> ~/gmod-1.0/load/bin/gmod_bulk_load_gff3.pl --organism dicty --gfffile
>>> chromosome_1.gff.sorted --noexon
>>>
>>> Produced the error:
>>>
>>> Can't locate object method "value" via package "Bio::Annotation::Target"
>>> at /Users/rns/gmod-1.0/load/bin/gmod_bulk_load_gff3.pl line 808, <GEN0>
>>> line 11.
>>>
>>>
>>> Is this due to the version of BioPerl I installed?  It looks like there
>>> is no value method on Bio::Annotation::Target.  I got the latest BioPerl
>>> by installing CJFIELDS/BioPerl-1.6.0.tar.gz with CPAN, the GMOD
>>> INSTALL.Chado docs said any version greater than 1.5.2.
>>>
>>> Do you think I should I install an older version of BioPerl or try GMOD
>>> scripts from cvs?
>>>
>>>
>>> Thanks,
>>> Richard.
>>>
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>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
> 
> 
> 

DDB0232428	Sequencing
Center	chromosome	1	4923596	.	+	.	ID=DDB0232428;Name=1
DDB0232428	.	gene	201217	202272	.	+	.	ID=AAC4;Name=AAC4
DDB0232428	.	gene	1614526	1615398	.	-	.	ID=AF134171_1;Name=AF134171_1
DDB0232428	.	gene	2962986	2963929	.	-	.	ID=AF135841;Name=AF135841
DDB0232428	.	gene	872490	873185	.	-	.	ID=CBP2;Name=CBP2
DDB0232428	.	gene	3249734	3250465	.	-	.	ID=CYP508E1_ps;Name=CYP508E1_ps;description=putative
pseudogene%3B related to the cytochrome P450 family
DDB0232428	.	gene	4697435	4699014	.	+	.	ID=CYP513A3;Name=CYP513A3
DDB0232428	.	gene	2256023	2257759	.	+	.	ID=CYP524A1;Name=CYP524A1
DDB0232428	.	gene	212712	214898	.	-	.	ID=ChLim;Name=ChLim;description=contains a N-terminal
Calponin Homology (CH) domain%2C 3 LIM domains%2C and 4 LIM-related domains (LRDs)
DDB0232428	.	gene	4418564	4419469	.	-	.	ID=DD7-1;Name=DD7-1;description=similar to discoidin
I%3B involved in O-glycosylation as identified by mRNA differential display%3B almost identical to its
upstream gene %3Ca href%3D%22%2Fdb%2Fcgi-bin%2Fgene_page.pl?primary_id%3DDDB_G0270212%22%3E%3Ci%3EDDB_G0270212%3C%2Fi%3E%3C%2Fa%3E
DDB0232428	.	EST_match	2795706	2796096	.	-	.	ID=DDB0011957;Target=DDB0011957 1 418;Gap=M390 
DDB0232428	.	EST_match	1663152	1663644	.	+	.	ID=DDB0011958;Target=DDB0011958 1 501;Gap=M492 
DDB0232428	.	EST_match	2112916	2113481	.	-	.	ID=DDB0011968;Target=DDB0011968 1 566;Gap=M565 
DDB0232428	.	EST_match	2114170	2114776	.	-	.	ID=DDB0011969;Target=DDB0011969 1 607;Gap=M606 
DDB0232428	.	EST_match	4831534	4831917	.	-	.	ID=DDB0011973;Target=DDB0011973 1 384;Gap=M383 
DDB0232428	.	EST_match	943073	943647	.	-	.	ID=DDB0011978;Target=DDB0011978 1 574;Gap=M574 
DDB0232428	.	EST_match	423993	425616	.	+	.	ID=DDB0011980;Target=DDB0011980 1 1045;Gap=M45
I414 M722 I178 M264 
DDB0232428	.	EST_match	2795701	2796326	.	-	.	ID=DDB0011987;Target=DDB0011987 1 627;Gap=M625 
DDB0232428	.	EST_match	2640303	2640927	.	+	.	ID=DDB0011988;Target=DDB0011988 1 485;Gap=M322
I164 M138 
DDB0232428	.	EST_match	2795720	2796231	.	-	.	ID=DDB0011993;Target=DDB0011993 1 530;Gap=M511 

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resources and data with the reach of the web. Download the Adobe AIR SDK and
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Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
software. With Adobe AIR, Ajax developers can use existing skills and code to
build responsive, highly engaging applications that combine the power of local
resources and data with the reach of the web. Download the Adobe AIR SDK and
Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com