Re: [Gmod-ajax] trouble with GFF3 parsing

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

2010/1/15 Mitch Skinner <mit...@be...>:
> 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.

Thanks, very much, Mitch.  I'll try that out and let you know.   To be
honest, the parser has given me a lot of hassle with other stuff (line
endings and memory use) so I might try out BED and see if that is any
better.


James