[Gmod-help] Re: [Gmod-gbrowse] GFF3 validation
Todd Harris
toddwharris at gmail.com
Sun Sep 20 19:45:13 EDT 2009
Hi Chris -
It's in Perl and is quite clean OO.
t
On Sun, Sep 20, 2009 at 5:21 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 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
>>>
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>>>
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>>>
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>>>
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>>>
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>>>
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>>>
>>>
>>>
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>>
>>
>> ------------------------------------------------------------------------------
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>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9-12, 2009. Register
>> now!
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>
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