Re: [SO-devel] GFF3 Specification

[Peter C. <p.j...@go...>]

On Tue, Feb 26, 2013 at 7:16 PM, Barry Moore
<bar...@ge...> wrote:
> Thanks Peter for the useful feedback.
>
> The reference to the Order tag is a mistake - it's text that snuck in
> somehow from another version of the document where we were
> exploring the possible solutions.  I'll take that out now.

Great.

> In the case of the multiple ##sequence-region directives for the same seqid.
> That was a clarification that I added thinking that it added clarity to the
> text without breaking backwards compatibility, but perhaps I was wrong.  In
> the example you describe why wouldn't you just pull out the the features
> that you want, but still allow the ##sequence-region to specify the full
> range?
>
> This:
>
> ##sequence-region chr1 10000 52000
>
> Instead of this:
>
> ##sequence-region chr1 10000 12000
> ##sequence-region chr1 50000 52000
>

Yes, with the proposed specification that's a reasonable alternative.

To be clear, I just pulled that example out of the air - but it
was based on thinking about the sort of manipulations one
might do with alignment data editing during lift-over between
assemblies or whatever. I wanted to flag this as (as far as
I recalled) the recent discussion about this proposal hadn't
come to any consensus.

The fact that Joachim Baran commented that he'd noticed
this in GVF data from Ensembl suggests this is more than
just a hypothetical usage, and it could be premature to ban
in the new revision of GFF3.

Joachim Baran wrote:
>>>
>>> I came across that syntax in Ensembl's GVF files
>>> recently.
>>>

Regards,

Peter