Re: [Gmod-ajax] trouble with GFF3 parsing

[Mitch S. <mit...@be...>]

On 01/13/2010 01:49 AM, James Casbon wrote:
>
> 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
>    

Yeah, that's 1.6.1; I think it's formatted that way so that textual 
comparisons of version strings give the right answer (e.g., when 
comparing 1.6.2 to 1.6.12).

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

Well, the idea was to use bioperl to deal with parsing GFF3 so that we 
wouldn't have to write our own GFF3 parser.  The problem was in bioperl 
in this particular case, but (if you haven't already) you could also see 
if your GFF3 validates:
http://dev.wormbase.org/db/validate_gff3/validate_gff3_online

The bug where some features at the end of the refseq wouldn't show up 
has been fixed in bioperl, although it'll be a little while before the 
fix gets released.  I've attached a patch that you could apply to your 
bioperl installation, or you could get this file:

http://code.open-bio.org/svnweb/index.cgi/bioperl/checkout/bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm?rev=16695

and replace the version you currently have installed.

That said, you can also use BED, or a database (although the database 
would have to be one that has a bioperl Bio::DB::(whatever) interface, 
like chado, Bio::DB::SeqFeature::Store, or Bio::DB::GFF).

I've been thinking about writing something to import data into JBrowse 
that doesn't use bioperl, but some of the interfaces in the JBrowse code 
have to be reworked a bit before that can happen.

Regards,
Mitch