Scott Cain | 15 Feb 20:18 2013
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Re: sequence-region directives in gff files

Hi Carnë,

Thanks for pointing this out; I was only sort of paying attention to
the FeatureIO discussion, and it hadn't occurred to me that my commit
was the problem.

I believe I've reproduced the functionality from that commit, and I
even added a test that makes use of the added method (yes, I know, it
surprised me too!).  All of the tests now pass for me in the FeatureIO
master.  I'm putting it on my todo list to check that the Chado loader
that makes use of Bio::FeatureIO still works as expected with the new
incarnation.

Thanks,
Scott

On Wed, Feb 13, 2013 at 5:22 AM, Carnë Draug <carandraug+dev <at> gmail.com> wrote:
> Hi Scott
>
> 3 years ago, the code for the Bio::SeqFeatureIO::* modules was split
> from bioperl-live into a separate repository[1]. Because the code was
> not removed from the bioperl-live repository, people ended up patching
> on both sides, leading to 2 branches of development. Last weekend I
> merged them back together with the exception of one commit that would
> not longer apply[2].
>
> This commit was authored by you with the following commit message:
> "tiny change to Bio::FeatureIO::gff to allow the gmod chado gff3 bulk
> loader to not choke when the gff file has ##sequence-region
> directives.  The loader is documented not to support this, but now it
> will quitely ignore those directives."
>
> Do you think you could take a look at it?
>
> Thank you,
> Carnë
>
> [1] https://github.com/bioperl/Bio-FeatureIO
> [2] https://github.com/bioperl/bioperl-live/commit/7218728b66ad297953676236077fd0ec757378c0

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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