[BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly

[Aaron J.Mackey]

Forgive me for a stupid question, but does GBrowse (v1.58) now support 
GFF3?  Namely, can I have start/stops in sub-feature coordinates in my 
input GFF3 and expect bp_load_gff.pl to behave properly (i.e. generate 
"canonical" top-level coordinates for storage)?  I didn't see anything 
in the documentation, so I was surprised to see some of the words in 
these posts ...

Thanks

On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote:

> Cool.  I'm heavily into making the HSP's output proper GFF3 today for
> some of the Gbrowse tools that I have been working on, so I will jump 
> in
> and do this over the next day or two.
>
> Cheers!
>
> Mark
>
> On Fri, 2004-01-09 at 14:49, Scott Cain wrote:
>> I think everything you wrote below is correct.  As far as I know, only
>> Allen and I have been working BTGFF's GFF3 code, and we haven't 
>> touched
>> the alignment portion, so I am not surprised that it is wrong.  I
>> suppose fixing BTGFF may break some tools, but I know that the chado
>> loader I wrote will handle it correctly :-)
>>
>> Thanks,
>> Scott
>>
>>
>> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote:
>>> On Fri, 2004-01-09 at 11:22, Scott Cain wrote:
>>>
>>>>   - be sure to use a SO term for the type (ie, match or one of its
>>>> children)
>>>
>>> So... actually the existing implementation of GFF3 in bioperl
>>> from Bio::Tools::GFF->new(-gff_version => 3)
>>> does not generate correctly formatted GFF3 for alignment features, 
>>> yeah?
>>>
>>> e.g. for column 9 of an alignment feature I get:
>>>
>>> 	Target=gi|2828774:54232..54206
>>>
>>> whereas I think I should be getting
>>>
>>> 	Target=gi|2828774+54232+54206
>>>
>>> In addition, it passes through all sorts of other tags that begin 
>>> with
>>> capital letters:
>>>
>>> 	Bits=46.1;FracId=0.962962962962963
>>>
>>> these should be
>>>
>>> 	bits=46.1;fracId=0.962962962962963
>>>
>>> if I am reading the spec correctly.
>>>
>>> Finally, the column-3 term that comes out is "similarity", but it 
>>> should be
>>> one of the *match terms.  Is that also correct?
>>>
>>> Please confirm that I am interpreting the GFF3 spec correctly for 
>>> these
>>> Alignment features and I would be happy to go in and fix things 
>>> (a.k.a. break
>>> everyone else's tools ;-) )
>>>
>>> Cheerio!
>>>
>>> Mark
>>>
> -- 
> Mark Wilkinson <markw at illuminae.com>
> Illuminae
>
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