#67 config file: limit features by source; set feature label - JBrowse

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#67 ✓resolved

config file: limit features by source; set feature label

Reported by Alexie Papanicolaou | September 28th, 2010 @ 05:44 AM

Hello

I have 2 small questions. I have this in my config file

  "track": "protein_match",
  "key": "BLAST",
  "feature": ["protein_match:TEST"],
    "subfeatures": true,
  "class": "transcript",
    "subfeature_classes": {
    "match_part": "est"
  },
}

a) Is there any way to have a custom label for a feature (either defined or e.g {name} ?)
b) I'm perplexed on why my feature line doesn't limit protein_match to TEST (attached screenshot). It matters not what I put after the colon: the track looks the same (all protein_match features appear). Am I missing smth?

oh, I guess looking at the screenshot you might see that the Track label obscures the feature label (feature starts at 1 of the reference)...

many thanks
alexie

screenshot.png 19.2 KB

Comments and changes to this ticket

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Alexie Papanicolaou October 2nd, 2010 @ 06:54 AM
Hello

I've troubleshooted this and it was a stupid mistake from my end (+ some Drupalesque nonsense of escaping -> arrows)

For posterity: To troubleshoot I used this function:

'extraData'=>array('test'=>'sub {shift->some Bio::SeqFeatureI::method();}') and the urlTemplate to print out the {test}

Would it be possible to somehow change the feature label (description)? That would help a bit with troubleshooting (wouldn't have to hover :-) )

thank you (pls feel free to close the ticket)
a
Mitch October 3rd, 2010 @ 01:10 PM
- State changed from “new” to “resolved”
You can create a custom feature label with the "label" setting in the config file. It should be a perl sub; it gets the bioperl object as its first argument, and it should return a string. For example, here's one config file entry that creates a custom label:
```
{
  "track": "ExampleFeatures",
  "key": "Example Features",
  "feature": ["remark"],
  "autocomplete": "all",
  "class": "feature2",
  "label": "sub { $_[0]->source . \" - \" . $_[0]->display_name }"
},
```
JBrowse August 17th, 2012 @ 01:47 PM
(from [2e77792938d1ef192c558bfae59e931974c79df9]) merge htmlfeature_layout branch, closes #67, closes #122 https://github.com/GMOD/jbrowse/commit/2e77792938d1ef192c558bfae59e...

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