Re: [Gmod-ajax] [apollo] Importing itemRgb column of bed files

[Colin <col...@gm...>]

Hi Antonin
I would use BEDTabix because the BED handling of flatfile-to-json doesn't
load the itemRgb info correctly as far as I can tell, but with BEDTabix,
it's fairly easy.

Example config for a BEDTabix track

{
  "label": "My track",
  "urlTemplate": "file.bed.gz",
  "storeClass": "JBrowse/Store/SeqFeature/BEDTabix",
  "style": { "color": "function(feature){return feature.get('itemrgb')}" }
}

-Colin



On Thu, Apr 13, 2023 at 11:03 AM Nathan Dunn <nd...@gm...> wrote:

>
> This is more of a JBrowse 1 question.
>
> Nathan
>
>
> On Apr 13, 2023, at 8:49 AM, Antonin Thiébaut <
> ant...@gm...> wrote:
>
> Hello all,
>
> I was wondering whether there is a way to import the itemRgb column of a
> bed file. I would like to use it to color the features.
>
> I am currently using the following command in Apollo v2.6.2 to create the
> bed tracks:
> perl -w bin/flatfile-to-json.pl --bed path/to/bed --trackLabel
> putative_orf --key "PCCR bacteria" --out data/bacteria/ --config '{
> "category": "Coding Potential" }' --trackType CanvasFeatures
>
> This successfully imports the file and there is no display problem on the
> browser, however I have the feeling it only imports the data of the first
> few columns of the file (I checked in the tracks directory that is created
> during the import). Can it be caused by an improper formatting or my file?
> Or am I missing an option in the command, is there another script to do
> this?
>
> Thank you in advance,
>
> *Antonin*
>
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