[Gmod-help] Re: [Gmod-gbrowse] GFF3 validation
Chris Fields
cjfields at illinois.edu
Sun Sep 20 19:21:10 EDT 2009
What is the validator written in? Just curious, but we have discussed
rewriting hunks of the bioperl GFF-related code, and I'm wondering if
this would fit in somehow or could be delegated to.
chris
On Sep 20, 2009, at 6:11 PM, Todd Harris wrote:
> 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
>>
>> 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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>
> ------------------------------------------------------------------------------
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> is the only developer event you need to attend this year. Jumpstart
> your
> developing skills, take BlackBerry mobile applications to market and
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> ahead of the curve. Join us from November 9-12, 2009. Register
> now!
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