Re: [Gmod-ajax] minimal gff

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

I thought about this some more and your use case seems like a reasonable 
one to me.  I tried out your patch in my working copy, and I noticed two 
things:

1. There's no documentation on those options in the help message
2. The "if" statement that prints out the usage message doesn't check 
for $gfffolder

If you prepare another patch that addresses those things, I'll apply it 
to jbrowse master.

Thanks for the patch,
Mitch

Giles Velarde wrote:
> In our case we export one GFF per top-level source feature in the 
> database. This can be a chromosome, but is more often a contig (and 
> there are lots of those). They could be concatenated into one big GFF 
> of course (I think GFF allows for that?).
>
>> If you're using GFF files with prepare-refseqs.pl then one option is 
>> to create one GFF file per organism with all of the sequence-region 
>> lines in it (and nothing else).  Running prepare-refseqs.pl on that 
>> file should be pretty fast.
>>
>
> Good idea, makes sense as that's the only thing that gets parsed at 
> that point (though I didn't know that at the time when I first started 
> looking).