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

[Todd Harris]

Hi Jim, Wes -

I've used our very own GFF3 validator on-and-off over the past two
years.  Although we have had some downtime with the validator due to
migrating services to a new hosting facility and new hardware, it is
functioning now.

Still, I think it makes sense for this service to be subsumed by GMOD,
with interested users assuming maintenance of the code.  The original
developer of the validator left WormBase years ago.  At that time,
there was some discussion of handover to GMOD but that clearly never
got very far.

Zheng Zha has made some changes (principally updating the version of
the sequence ontology file; the WormBase validator uses a very old
version).  This represents the most logical branch of code for import
to the GMOD repository.

I'm happy to check it in and help set up an instance on GMOD.org if I
can get shell access to the machine.

Todd




On Sun, Sep 20, 2009 at 4:25 PM, Jim Hu <jimhu at tamu.edu> 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.
> 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
>
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>
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>
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>
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>
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