[Bioperl-l] [SO-devel] GFF3 Validator

chris mungall cjm at fruitfly.org
Thu Apr 13 23:42:55 EDT 2006


There's also a script in cvs/song/software/scripts/ 
validate_features.pl - it focuses purely on validating the parent/ 
child relationships w.r.t SO

It uses Bio::Tools::GFF, it should probably be updated to use the  
latest bioperl code

On Apr 13, 2006, at 8:32 PM, Suzanna Lewis wrote:

> That is nice. Thanks for the pointer.
>
> -S
>
> On Apr 9, 2006, at 1:37 PM, Lincoln Stein wrote:
>
>> Hi All,
>>
>> I just wanted to draw your attention to a GFF3 validator put up by  
>> the NIAID
>> BRC program. It checks that the GFF3 file is well formed and that  
>> only SO
>> terms are used in the feature type column. It doesn't check that  
>> parent/child
>> relationships follow the spec, but it is a real good start.
>>
>> The documentation: http://iowg.brcdevel.org/gff3.html
>> Standalone script: http://iowg.brcdevel.org/gff3validator/
>> Web-based script:
>> 	http://www.tigr.org/tigr-scripts/prok_manatee/brc-central/ 
>> gff_validation.cgi
>>
>> Lincoln
>>
>> -- 
>> Lincoln D. Stein
>> Cold Spring Harbor Laboratory
>> 1 Bungtown Road
>> Cold Spring Harbor, NY 11724
>> (516) 367-8380 (voice)
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>> PLEASE CONTACT MY ASSISTANT,
>> SANDRA MICHELSEN, AT michelse at cshl.edu
>>
>>
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>
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