[Gmod-gbrowse] [Gmod-help] Re: [Gmod-schema] Error loading GFF3 file into chado

[Shengqiang Shu]

This file is in format of GFF3, Is this loading problem due to file  
not conforming to GFF3 standard? In term of SO terms, it uses gene,  
mRNA, exon, CDS. No problem, is there?

Only thing looks like missing is Name attribute. Is Name attribute  
required? From scanning through doc on sequence ontology site, it did  
not say Name is required.

I know this file is produced by one of our members. If you guys point  
out what is the problem with file in term of conforming to GFF3  
standard, it would be very helpful.

By the way, FASTA in GFF3 is optional, isn't? Don't know why loader  
can not handle it? ah, the file is annotation GFF3 file, it does not  
contain genomic features. Is this causing the loading problem?


Shu


On Aug 14, 2009, at 12:54 PM, Chris Fields wrote:

> Yikes, another GFF2 variant?
>
> chris
>
> On Aug 14, 2009, at 2:50 PM, Jason Stajich wrote:
>
>> I also have these script jg_gff2gff3.pl in gff_tools of http://github.com/hyphaltip/genome-scripts/tree/master
>> and
>> gff3_to_JGIgff.pl for converting back into JGI gff from GFF3.
>>
>> -jason
>>
>> On Aug 14, 2009, at 11:01 AM, Don Gilbert wrote:
>>
>>>
>>>> Has anyone out there written a JGI GFF2 to GFF3 parser
>>>
>>> I've written both ways: jgi to gff3, and gff3 to jgi-gff (which is a
>>> variant of gff2).
>>> Find here
>>> http://wfleabase.org/release1/current_release/supplement/jgi_gff/
>>> as jgi2gff.pl  (and dpulex_gff2jgi.pl  for the other way)
>>>
>>> This script will want some revision for your data, and the variant
>>> of JGI's gff
>>> I worked with may differ from yours.  Look at the sample at the top
>>> of the
>>> script to see if it matches yours.
>>>
>>> - Don
>>>
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>>
>> --
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>>
>>
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