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

[Jim Hu]

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.

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>  
> 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>
>>
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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


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