Re: Gmod-ajax Digest, Vol 95, Issue 27

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Re: Gmod-ajax Digest, Vol 95, Issue 27

kkarra@stanford.edu
Never mind. 

  if (typeof orf_classification === 'undefined'){ orf_classification = ''; }

With the addition of that line, it seems better..I must have used 2 equal signs..

On Sep 26, 2016, at 3:21 PM, [hidden email] wrote:

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Today's Topics:

  1. GMOD & JBrowse user survey, 2016 (Ian Holmes)
  2. features color (Kalpana Karra)


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Message: 1
Date: Thu, 22 Sep 2016 18:54:31 -0700
From: Ian Holmes <[hidden email]>
Subject: [Gmod-ajax] GMOD & JBrowse user survey, 2016
To: "[hidden email]"
<[hidden email]>
Message-ID:
<[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hello JBrowse users,

The following survey is aimed at users (and potential users) of GMOD genome
databases, especially the JBrowse genome browser. It will directly inform
the priorities for renewal of the R01 that funds JBrowse software
development and the GMOD helpdesk.

We know surveys are thankless and dull. Your time in filling out this one
is GREATLY appreciated.

https://goo.gl/forms/1bKIuAMjGKrS0hUi1

Thanks & best wishes,
The JBrowse team
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Message: 2
Date: Mon, 26 Sep 2016 15:21:13 -0700
From: Kalpana Karra <[hidden email]>
Subject: [Gmod-ajax] features color
To: [hidden email]
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="utf-8"

I am trying to display canvas features in different colors based on the value in column 9. I tried many different things, but, I don?t see the colors I have in functions.conf

Wondering where I am going wrong.. this link seems to indicate the value should be accessible by name and since there are no comma separated, I am assuming I get a string back..

http://gmod.org/wiki/JBrowse_FAQ#How_do_I_access_data_about_my_features_in_my_callback_or_plugin <http://gmod.org/wiki/JBrowse_FAQ#How_do_I_access_data_about_my_features_in_my_callback_or_plugin>

Thanks!
-Kalpana

P.S. I looked at http://staging.wormbase.org/tools/genome/jbrowse/data/functions.conf <http://staging.wormbase.org/tools/genome/jbrowse/data/functions.conf> and think I am trying similar thing



GFF example line: (not all lines have orf_classification value)
================

chrI    SGD     gene    13363   13743   .       -       .       ID=YAL064C-A;Name=YAL064C-A;gene=TDA8;Alias=TDA8,YAL065C-A;Ontology_term=GO:0003674,GO:0005575,GO:0008150;Note=Putative%20protein%20of%20unknown%20function%3B%20null%20mutant%20is%20sensitive%20to%20expression%20of%20the%20top1-T722A%20allele%3B%20not%20an%20essential%20gene;display=Putative%20protein%20of%20unknown%20function;dbxref=SGD:S000002140;orf_classification=Uncharacterized


trackList.json:
===============

     {
        "label" : "All Annotated Sequence Features",
        "trackType" : "CanvasFeatures",
        "key" : "All Annotated Sequence Features",
        "storeClass" : "JBrowse/Store/SeqFeature/NCList",
        "style" : {
           "description" : "description,note",
           "className" : "feature",
           "label" : "gene,name,id",
           "color" : "{geneColor}"
        },
        "type" : "CanvasFeatures",
        "glyph" : "JBrowse/View/FeatureGlyph/Box",
        "fmtDetailValue_Name" : "function(name, feature) {if(feature.get('type')=='gene') {return '<a href=\"http://www.yeastgenome.org/locus/'+name+'/overview\">'+name+'</a>';} else { return name;}}",
        "urlTemplate" : "tracks/All Annotated Sequence Features/{refseq}/trackData.json",
        "compress" : 0
     },


functions.conf:
==============
geneColor = function(feature) {
   var orf_class = feature.get('orf_classification');
   if (orf_class.match(/Dubious/i))    {return 'lightgrey';}
   if (orf_class.match(/Uncharacterized/i)) {return 'peachpuff';}
   if (orf_class.match(/Verified/i))    {return 'red';}
   if (orf_class.match(/silenced_gene:Verified/i))  {return 'green';}
   if (orf_class.match(/silenced_gene/i))  {return 'brown';}
   return 'wheat'; }




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