Re: [Gmod-ajax] trouble with GFF3 parsing

[James C. <ca...@gm...>]

2010/1/12 Mitch Skinner <mit...@be...>:
> On 01/12/2010 02:29 AM, James Casbon wrote:
>>
>> Changing the sequence-region pragma to be a larger region fixes the
>> problem:
>> ##sequence-region CYP2C8 1 46725
>>
>> What is going on here?  Why do I not get all the features I declared?
>>
>
> Thanks for providing such a nice clean test case.
>
> This sounds like it might be related to an issue in
> Bio::DB::SeqFeature::Store::memory that was fixed last year after bioperl
> 1.6 was released.  The fix is in bioperl 1.6.1, though--what version are you
> using?
>
> Also, JBrowse used to need the sequence-region line, but in the current code
> it's no longer required.  So one work-around if you can't upgrade bioperl
> would be to leave out the sequence-region line, I think.

I think you are right that it may be a problem with bioperl, but I am
fairly certain I am on 1.61, although this is confusing:
$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006001

Is there any way to load data that doesn't go via bioperl?  My
experience getting GFF3 to parse has not been joyful.

cheers,
James