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

[Aaron J.Mackey]

Hi Scott,

Thanks for the quick reply, but that wasn't exactly the nature of the  
question; the question was whether (apart from Gap attributes), do  
gbrowse, BDGFF, and/or, specifically, load_gff.pl variants know the  
rest of GFF3, namely to provide the ability of input GFF3 with features  
that aren't in absolute reference coordinates, but in relative  
coordinates?  And is that ability in release 1.58, or some CVS branch I  
can access (code that lives quietly in the depths of Lincoln's hard  
drive doesn't count)?

Thanks,

-Aaron

On Jan 9, 2004, at 4:47 PM, Scott Cain wrote:

> OK, I am going to answer this, but if I am wrong, I'm sure Lincoln will
> correct me.  I don't think gbrowse or BDGFF knows how to deal with  
> cigar
> lines in Gap attributes yet.  It is safer for the moment to continue to
> put separate HSPs on separate GFF lines for the time being.
>
> Scott
>
>
> On Fri, 2004-01-09 at 16:42, Aaron J.Mackey wrote:
>> 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
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
> --  
> ----------------------------------------------------------------------- 
> -
> Scott Cain, Ph. D.                                          
> cain at cshl.org
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
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