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

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

That helped. With this new GFF file,

##gff-version 3
NC_004578	GenBank	gene	8438	15223	.	+	1	ID=1489763
NC_004578	GenBank	CDS	9000	10000	.	+	1	Parent=1489763
NC_004578	GenBank	CDS	11000	12000	.	+	1	Parent=1489763

and this command,

./bin/flatfile-to-json.pl --gff test.gff \
    --getType --getSubs --tracklabel test --key test \
    --subfeatureClasses '{"CDS": "transcript-CDS"}'

I am closer to the resutls that I want.

Thank you.

On Fri, Aug 6, 2010 at 1:10 PM, Scott Cain <sc...@sc...> wrote:
> Hi Paul,
>
> Off hand, I don't know the details of JBrowse configuration, but I can
> tell you that you GFF is wrong.  The Parent part should look like the
> ID part, with tag=value, so the ninth column should look like this
> "ID=9695423;Parent=1489763".  Also, there is no need for the CDS
> features to have an ID unless those features have children as well;
> IDs are only for identifying parent-child relationships.  You might
> find the GFF3 validator useful:
>
>  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online
>
> Scott
>
>
> On Fri, Aug 6, 2010 at 12:05 PM, Paul Stodghill
> <pau...@gm...> wrote:
>> I'm trying to create a feature track that contains nested features,
>> similar to the mRNA track in the Drosophila.
>>
>> Here is the GFF file that I am using as input,
>>
>> ##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"}'
>>
>> I can see that both trackData.json and subfeatures-1.json are being
>> created in the right track directory.
>>
>> Here is what gets inserted into trackInfo.js
>>
>>   {
>>      "url" : "data/tracks/{refseq}/test/trackData.json",
>>      "type" : "FeatureTrack",
>>      "label" : "test",
>>      "key" : "test"
>>   }
>>
>> For starters, I see that "subfeatures":true needs to be added to
>> trackInfo.js, but what else?
>>
>> (I tried following the configuration provided for the Drosophila, but
>> the syntax used for that example and for the for the config file
>> reference documentation appear to be out of sync with the current
>> implementation.)
>>
>> Thanks.
>>
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>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>