[Gmod-help] Re: [Gmod-gbrowse] GFF3 validation

[Wes Barris]

Jim Hu wrote:
> The Wormbase gff validator has been down for a long time.  The pathogen 
> portal one is not very good.  The one that should be at Wormbase should 
> be available somewhere in the (formerly cvs) svn repository.  

Yes, the pathogen one has some problems.

I found another working validator here:

http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

> I should try to put a copy up on one of our public servers.
> 
> Jim
> 
> On Sep 14, 2009, at 11:41 PM, Dave Clements, GMOD Help Desk wrote:
> 
>> Hi Wes,
>>
>> Thanks for the heads up on the GFF3 validator at WormBase.  I don't
>> know what happened to it, but I'll investigate, and drop the link.
>>
>> For the validator from pathogenportal, try dropping everything between
>> line 2 and the line that says =cut.
>>
>> Thanks,
>>
>> Dave C
>>
>> On Mon, Sep 14, 2009 at 8:47 PM, Wes Barris <wes.barris at csiro.au 
>> <mailto:wes.barris at csiro.au>> wrote:
>>> Hi,
>>>
>>> The GFF3 validation link to wormbase on this page:
>>>
>>> http://gmod.org/wiki/GFF3#GFF3_Validation
>>>
>>> results in an error.  I don't know whether or not wormbase is still
>>> providing a gff3 validator.
>>>
>>> Also, the gff3 validation perl code from the same page:
>>>
>>> http://www.pathogenportal.org/resources/gff3Valid.pl
>>>
>>> has errors in it:
>>>
>>> perl -c gff3Valid.pl
>>> Number found where operator expected at gff3Valid.pl line 8, near 
>>> "GFF3 1.01"
>>>         (Do you need to predeclare GFF3?)
>>> Bareword found where operator expected at gff3Valid.pl line 8, near 
>>> "1.01 spec"
>>>         (Missing operator before spec?)
>>> Bareword found where operator expected at gff3Valid.pl line 10, near 
>>> "//www"
>>>         (Missing operator before www?)
>>> Number found where operator expected at gff3Valid.pl line 22, near 
>>> "over 4"
>>>         (Do you need to predeclare over?)
>>> syntax error at gff3Valid.pl line 8, near "GFF3 1.01"
>>> Unmatched right curly bracket at gff3Valid.pl line 190, at end of line
>>> syntax error at gff3Valid.pl line 190, near "}"
>>> gff3Valid.pl had compilation errors.
>>>
>>> --
>>> Wes Barris <wes.barris at csiro.au <mailto:wes.barris at csiro.au>>
>>>
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>>
>>
>>
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> 
> =====================================
> 
> Jim Hu
> 
> Associate Professor
> 
> Dept. of Biochemistry and Biophysics
> 
> 2128 TAMU
> 
> Texas A&M Univ.
> 
> College Station, TX 77843-2128
> 
> 979-862-4054
> 
> 
> 


-- 
Wes Barris <wes.barris at csiro.au>