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Feature display bug when setting description="score" #673

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erasche opened this Issue Dec 28, 2015 · 3 comments

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@erasche
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erasche commented Dec 28, 2015

With "description": "":

selection_520

With "description": "score":
selection_519

gff3:

test.gff.txt

##gff-version 3
##sequence-region Merlin 1 172788
Merlin  blast   protein_match   752 1039    9.23754e-17 +   .   _Hit_id=gi|308814559|ref|YP_003934833.1|;_Length=107;_Accession=YP_003934833;_Hit_titles=gi|308814559|ref|YP_003934833.1| hypothetical protein SP18_gp210 [Shigella phage SP18],gi|308206151|gb|ADO19550.1| hypothetical protein SP18gp210 [Shigella phage SP18];_Description=hypothetical protein SP18_gp210 [Shigella phage SP18];ID=biopygen4
Merlin  blast   match_part  752 1036    .   +   .   Gap=M95;ID=gi|308814559|ref|YP_003934833.1|;Parent=biopygen4
Merlin  blast   protein_match   752 1039    7.7684e-16  +   .   _Description=Alt.-3 conserved hypothetical protein [Enterobacteria phage vB_EcoM-VR7];ID=biopygen7;_Hit_id=gi|314121774|ref|YP_004063893.1|;_Accession=YP_004063893;_Hit_titles=gi|314121774|ref|YP_004063893.1| Alt.-3 conserved hypothetical protein [Enterobacteria phage vB_EcoM-VR7],gi|313151531|gb|ADR32587.1| Alt.-3 conserved hypothetical protein [Enterobacteria phage vB_EcoM-VR7];_Length=96
Merlin  blast   match_part  752 1036    .   +   .   Gap=M95;ID=gi|314121774|ref|YP_004063893.1|;Parent=biopygen7
###
Merlin  blast   protein_match   752 1039    2.41009e-15 +   .   ID=biopygen8;_Description=Alt.-3 conserved hypothetical protein [Enterobacteria phage JS98];_Accession=YP_001595321;_Hit_titles=gi|161622625|ref|YP_001595321.1| Alt.-3 conserved hypothetical protein [Enterobacteria phage JS98],gi|52139951|gb|AAU29321.1| Alt.-3 conserved hypothetical protein [Enterobacteria phage JS98];_Length=96;_Hit_id=gi|161622625|ref|YP_001595321.1|
Merlin  blast   match_part  752 1036    .   +   .   ID=gi|161622625|ref|YP_001595321.1|;Gap=M95;Parent=biopygen8
Merlin  blast   protein_match   752 1036    2.9568e-16  +   .   _Hit_id=gi|456351278|ref|YP_007501230.1|;_Accession=YP_007501230;_Hit_titles=gi|456351278|ref|YP_007501230.1| hypothetical protein [Salmonella phage S16],gi|448913695|gb|AGE48199.1| hypothetical protein [Salmonella phage S16];_Length=106;_Description=hypothetical protein [Salmonella phage S16];ID=biopygen5
Merlin  blast   match_part  752 1033    .   +   .   ID=gi|456351278|ref|YP_007501230.1|;Gap=M94;Parent=biopygen5
###
Merlin  blast   protein_match   752 1036    5.19436e-16 +   .   _Hit_id=gi|408387127|gb|AFU64136.1|;_Length=96;_Accession=AFU64136;_Hit_titles=gi|408387127|gb|AFU64136.1| hypothetical protein [Salmonella phage STML-198];_Description=hypothetical protein [Salmonella phage STML-198];ID=biopygen6
Merlin  blast   match_part  752 1033    .   +   .   ID=gi|408387127|gb|AFU64136.1|;Gap=M94;Parent=biopygen6

full track config (from web side):

{
  "maxFeatureSizeForUnderlyingRefSeq": 250000,
  "maxFeatureScreenDensity": 0.5,
  "glyph": "JBrowse/View/FeatureGlyph/Segments",
  "maxFeatureGlyphExpansion": 500,
  "maxHeight": 600,
  "histograms": {
    "description": "feature density",
    "min": 0,
    "height": 100,
    "color": "goldenrod",
    "clip_marker_color": "red"
  },
  "style": {
    "_defaultHistScale": 4,
    "_defaultLabelScale": 30,
    "_defaultDescriptionScale": 120,
    "showLabels": true,
    "showTooltips": true,
    "label": "Description",
    "description": "",
    "className": "feature"
  },
  "displayMode": "normal",
  "events": {},
  "menuTemplate": [
    {
      "label": "View details",
      "title": "{type} {name}",
      "action": "contentDialog",
      "iconClass": "dijitIconTask"
    },
    {
      "iconClass": "dijitIconConnector"
    },
    {
      "iconClass": "dijitIconFilter"
    }
  ],
  "type": "JBrowse/View/Track/CanvasFeatures",
  "urlTemplate": "tracks/c3979698f4adbbbdba3d4df03b392167_0/{refseq}/trackData.json",
  "key": "BlastP",
  "category": "Blah",
  "label": "c3979698f4adbbbdba3d4df03b392167_0",
  "compress": 0,
  "storeClass": "JBrowse/Store/SeqFeature/NCList",
  "trackType": "JBrowse/View/Track/CanvasFeatures",
  "baseUrl": "http://localhost:8000/out/data/",
  "metadata": {}
}

can provide more information on request :)

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enuggetry Jan 4, 2016

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Thanks for the catch.

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enuggetry commented Jan 4, 2016

Thanks for the catch.

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cmdcolin Feb 27, 2016

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Looks like this was reproducible and just needed to stringify the label/description! See 6182912

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cmdcolin commented Feb 27, 2016

Looks like this was reproducible and just needed to stringify the label/description! See 6182912

@cmdcolin cmdcolin closed this Feb 27, 2016

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erasche Feb 28, 2016

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Wow, thanks @cmdcolin!

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erasche commented Feb 28, 2016

Wow, thanks @cmdcolin!

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