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

Jim Hu jimhu at tamu.edu
Mon Sep 21 00:08:46 EDT 2009 

Hi Todd,

Sorry!  I should have confirmed that it was still down before replying  
to Wes.  Glad it's back up.  It trances for me with the default  
selection for the SO file, but works if I pick SOFA latest.

Subsuming into gmod.org or into the SO project (that's where the top  
Google hit for GFF3 spec is) would make a lot of sense.  I downloaded  
the trunk version from sourceforge and it was pretty easy to get it  
working on our server:

	http://ecolihub.net/cgi-bin/validate_gff3_online/validate_gff3_online

It looks like the one at Wormbase may still be Payan's.  The one from  
trunk looks like Zheng's.  At least it has a different version number.  
It was pretty easy to set up, but I did have to make one change that  
may be a Mac Perl dialect thing.  In GFF::Online.pm I had to change

     my $file_length = `wc -l $report_file` =~ /^(\d+)/;

in sub _store_report_file_info to two lines

     my $file_length = `wc -l $report_file`;
     $file_length =~ /^(\d+)/;

There may be a few other things to tweak.  I'm trying to figure out  
how it decides what the latest SO.obo file is.

Jim

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
>>
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry&reg; Developer Conference in SF,  
>> CA
>> is the only developer event you need to attend this year. Jumpstart  
>> your
>> developing skills, take BlackBerry mobile applications to market  
>> and stay
>> ahead of the curve. Join us from November 9&#45;12, 2009. Register  
>> now&#33;
>> http://p.sf.net/sfu/devconf
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>

=====================================
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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