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

[Antonin T. <ant...@gm...>]

Hi Colin,

Thanks for the advice, the BEDTabix track upload worked great!

Antonin


Le vendredi 14 avril 2023 à 19:46:59 UTC+2, Colin a écrit :

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 <ndu...@gmail.com> wrote:


This is more of a JBrowse 1 question. 

Nathan 


On Apr 13, 2023, at 8:49 AM, Antonin Thiébaut <antonin.t...@gmail.com> 
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*

-- 
To unsubscribe from this group and stop receiving emails from it, send an 
email to apollo+un...@lbl.gov.


-- 
To unsubscribe from this group and stop receiving emails from it, send an 
email to apollo+un...@lbl.gov.