Re: [Gmod-ajax] I give up. What is the magic to get subfeatures?

[Paul S. <pau...@gm...>]

Using --gff instead of --gff2 helps too. Thanks.

On Fri, Aug 6, 2010 at 1:51 PM, Mitch Skinner
<mit...@be...> wrote:
>  And once you've made the modifications that Scott recommends, it may help
> to change the --gff2 parameter to --gff.  In this case, "--gff" means GFF3.
>  When I wrote that code, I guess I was thinking of GFF3 as being the typical
> version of GFF.  GFF3 was the first version JBrowse supported, anyway, and
> when I added a separate code path for GFF2 then I added the --gff2
> parameter.
>
> It's like the first part of the flatfile-to-json.pl usage message says:
>
> USAGE: bin/flatfile-to-json.pl [--gff <gff3 file> | --gff2 <gff2 file> |
> --bed <bed file>]
>
> Sorry for any confusion,
> Mitch
>
> On 08/06/2010 09:05 AM, Paul Stodghill wrote:
>>
>> ##gff-version 3
>> NC_004578       GenBank gene    8438    15223   .       +       1
>> ID=1489763;
>> NC_004578       GenBank CDS     9000    10000   .       +       1
>> ID=9695423; Parent:1489763;
>> NC_004578       GenBank CDS     11000   12000   .       +       1
>> ID=9695424; Parent:1489763;
>>
>> Here is how I am invoking  flatfile-to-json.pl,
>>
>> ./bin/flatfile-to-json.pl --gff2 test.gff --getType --getSubs
>> --tracklabel test --key test --subfeatureClasses '{"CDS":
>> "transcript-CDS"}'
>>
>
>