[Gmod-ajax] Segments glyph config

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[Gmod-ajax] Segments glyph config

Scott Cain
Hi All,

Another day, another "I think I've almost got it" moment.  I'm working on this browser:

http://dev.wormbase.org:9003/jbrowse/?data=data%2Fc_elegans&loc=X%3A7517701..7603000&tracks=Gene%20Models%20(historical)%2CCurated%20Genes&highlight=

and I used this command to process data:

bin/flatfile-to-json.pl \
    --gff ../c_elegans_gff/X.c_elegans.gff3 --out data/c_elegans \
    --type pseudogenic_transcript:history,transposable_element:history,protein_coding_primary_transcript:history,primary_transcript:history,nc_primary_transcript:history \
    --trackLabel "Gene Models (historical)" --trackType CanvasFeatures \
    --key "Gene Models (historical)"

Note that there are many parent types, none of which are "typical".  The data are pretty straight forward:

X   history protein_coding_primary_transcript   7551372 7554419 .   -    .       ID=CDS:F46C8.8:wp108;Name=F46C8.8:wp108
X   history exon    7551372 7551463 .   -   .   Parent=CDS:F46C8.8:wp108
X   history exon    7551507 7551674 .   -   .   Parent=CDS:F46C8.8:wp108

I haven't done much fancy with the config either:

      {
         "style" : {
            "className" : "feature",
            "glyph" : "JBrowse/View/FeatureGlyph/Segments",
            "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
            "subfeatureClasses" : {
               "exon" : "transcript-CDS"
            },
         },
         "key" : "Gene Models (historical)",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Not Good",
         "type" : "CanvasFeatures",
         "label" : "Gene Models (historical)"
      },

I've tried with and without the subfeatureClasses option, and with transcript-CDS and transcript-exon and several other things as well that didn't work.  What I get is a solid rectangle that represents the extents of the parent feature and I can never get the exons to draw.  Can anybody please point out what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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Re: Segments glyph config

Colin
I think you need to set "subParts": "exon" in this track. The style->subfeatureClasses is for HTMLFeatures based rendering. You can see the configuration options here and compare the CanvasFeatures with HTMLFeatures configuration options here http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options

-Colin


On Thu, Jun 26, 2014 at 1:06 PM, Scott Cain <[hidden email]> wrote:
Hi All,

Another day, another "I think I've almost got it" moment.  I'm working on this browser:

http://dev.wormbase.org:9003/jbrowse/?data=data%2Fc_elegans&loc=X%3A7517701..7603000&tracks=Gene%20Models%20(historical)%2CCurated%20Genes&highlight=

and I used this command to process data:

bin/flatfile-to-json.pl \
    --gff ../c_elegans_gff/X.c_elegans.gff3 --out data/c_elegans \
    --type pseudogenic_transcript:history,transposable_element:history,protein_coding_primary_transcript:history,primary_transcript:history,nc_primary_transcript:history \
    --trackLabel "Gene Models (historical)" --trackType CanvasFeatures \
    --key "Gene Models (historical)"

Note that there are many parent types, none of which are "typical".  The data are pretty straight forward:

X   history protein_coding_primary_transcript   7551372 7554419 .   -    .       ID=CDS:F46C8.8:wp108;Name=F46C8.8:wp108
X   history exon    7551372 7551463 .   -   .   Parent=CDS:F46C8.8:wp108
X   history exon    7551507 7551674 .   -   .   Parent=CDS:F46C8.8:wp108

I haven't done much fancy with the config either:

      {
         "style" : {
            "className" : "feature",
            "glyph" : "JBrowse/View/FeatureGlyph/Segments",
            "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
            "subfeatureClasses" : {
               "exon" : "transcript-CDS"
            },
         },
         "key" : "Gene Models (historical)",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Not Good",
         "type" : "CanvasFeatures",
         "label" : "Gene Models (historical)"
      },

I've tried with and without the subfeatureClasses option, and with transcript-CDS and transcript-exon and several other things as well that didn't work.  What I get is a solid rectangle that represents the extents of the parent feature and I can never get the exons to draw.  Can anybody please point out what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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Re: Segments glyph config

Richard Hayes
subParts in place of subfeatureClasses was going to be my suggestion. I've found that subParts is nearly always required to tell JBrowse what to render as subfeatures, unless you have a very "standard" GFF3 format as input.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov


On Thu, Jun 26, 2014 at 11:20 AM, Colin <[hidden email]> wrote:
I think you need to set "subParts": "exon" in this track. The style->subfeatureClasses is for HTMLFeatures based rendering. You can see the configuration options here and compare the CanvasFeatures with HTMLFeatures configuration options here http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options

-Colin


On Thu, Jun 26, 2014 at 1:06 PM, Scott Cain <[hidden email]> wrote:
Hi All,

Another day, another "I think I've almost got it" moment.  I'm working on this browser:

http://dev.wormbase.org:9003/jbrowse/?data=data%2Fc_elegans&loc=X%3A7517701..7603000&tracks=Gene%20Models%20(historical)%2CCurated%20Genes&highlight=

and I used this command to process data:

bin/flatfile-to-json.pl \
    --gff ../c_elegans_gff/X.c_elegans.gff3 --out data/c_elegans \
    --type pseudogenic_transcript:history,transposable_element:history,protein_coding_primary_transcript:history,primary_transcript:history,nc_primary_transcript:history \
    --trackLabel "Gene Models (historical)" --trackType CanvasFeatures \
    --key "Gene Models (historical)"

Note that there are many parent types, none of which are "typical".  The data are pretty straight forward:

X   history protein_coding_primary_transcript   7551372 7554419 .   -    .       ID=CDS:F46C8.8:wp108;Name=F46C8.8:wp108
X   history exon    7551372 7551463 .   -   .   Parent=CDS:F46C8.8:wp108
X   history exon    7551507 7551674 .   -   .   Parent=CDS:F46C8.8:wp108

I haven't done much fancy with the config either:

      {
         "style" : {
            "className" : "feature",
            "glyph" : "JBrowse/View/FeatureGlyph/Segments",
            "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
            "subfeatureClasses" : {
               "exon" : "transcript-CDS"
            },
         },
         "key" : "Gene Models (historical)",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Not Good",
         "type" : "CanvasFeatures",
         "label" : "Gene Models (historical)"
      },

I've tried with and without the subfeatureClasses option, and with transcript-CDS and transcript-exon and several other things as well that didn't work.  What I get is a solid rectangle that represents the extents of the parent feature and I can never get the exons to draw.  Can anybody please point out what I'm doing wrong?

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
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Re: Segments glyph config

Scott Cain
Hi Richard and Colin,

After deleting and recreating the data, deleting cookies and caches (which I don't think I have to do in Chrome with the developer's console is open, right?), and changing the track config to this:

      {
         "style" : {
            "className" : "feature",
            "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
            "glyph" : "JBrowse/View/FeatureGlyph/Segments"
         },
         "subParts" : "exon",
         "key" : "Gene Models (historical)",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
         "compress" : 0,
         "label" : "Gene Models (historical)",
         "type" : "CanvasFeatures",
         "category" : "Not Good"
      },


Nothing changed :-/  Did I not do it right?  I tried subParts both in and out of the style section, but the docs imply that it should be out.

Thanks,
Scott





On Thu, Jun 26, 2014 at 2:43 PM, Richard Hayes <[hidden email]> wrote:
>
> subParts in place of subfeatureClasses was going to be my suggestion. I've found that subParts is nearly always required to tell JBrowse what to render as subfeatures, unless you have a very "standard" GFF3 format as input.
>
> Richard D. Hayes, Ph.D.
> Joint Genome Institute / Lawrence Berkeley National Lab
> http://phytozome.jgi.doe.gov
>
>
> On Thu, Jun 26, 2014 at 11:20 AM, Colin <[hidden email]> wrote:
>>
>> I think you need to set "subParts": "exon" in this track. The style->subfeatureClasses is for HTMLFeatures based rendering. You can see the configuration options here and compare the CanvasFeatures with HTMLFeatures configuration options here http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options
>>
>> -Colin
>>
>>
>> On Thu, Jun 26, 2014 at 1:06 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi All,
>>>
>>> Another day, another "I think I've almost got it" moment.  I'm working on this browser:
>>>
>>> http://dev.wormbase.org:9003/jbrowse/?data=data%2Fc_elegans&loc=X%3A7517701..7603000&tracks=Gene%20Models%20(historical)%2CCurated%20Genes&highlight=
>>>
>>> and I used this command to process data:
>>>
>>> bin/flatfile-to-json.pl \
>>>     --gff ../c_elegans_gff/X.c_elegans.gff3 --out data/c_elegans \
>>>     --type pseudogenic_transcript:history,transposable_element:history,protein_coding_primary_transcript:history,primary_transcript:history,nc_primary_transcript:history \
>>>     --trackLabel "Gene Models (historical)" --trackType CanvasFeatures \
>>>     --key "Gene Models (historical)"
>>>
>>> Note that there are many parent types, none of which are "typical".  The data are pretty straight forward:
>>>
>>> X   history protein_coding_primary_transcript   7551372 7554419 .   -    .       ID=CDS:F46C8.8:wp108;Name=F46C8.8:wp108
>>> X   history exon    7551372 7551463 .   -   .   Parent=CDS:F46C8.8:wp108
>>> X   history exon    7551507 7551674 .   -   .   Parent=CDS:F46C8.8:wp108
>>>
>>> I haven't done much fancy with the config either:
>>>
>>>       {
>>>          "style" : {
>>>             "className" : "feature",
>>>             "glyph" : "JBrowse/View/FeatureGlyph/Segments",
>>>             "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
>>>             "subfeatureClasses" : {
>>>                "exon" : "transcript-CDS"
>>>             },
>>>          },
>>>          "key" : "Gene Models (historical)",
>>>          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
>>>          "trackType" : "CanvasFeatures",
>>>          "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
>>>          "compress" : 0,
>>>          "category" : "Not Good",
>>>          "type" : "CanvasFeatures",
>>>          "label" : "Gene Models (historical)"
>>>       },
>>>
>>> I've tried with and without the subfeatureClasses option, and with transcript-CDS and transcript-exon and several other things as well that didn't work.  What I get is a solid rectangle that represents the extents of the parent feature and I can never get the exons to draw.  Can anybody please point out what I'm doing wrong?
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> Open source business process management suite built on Java and Eclipse
>>> Turn processes into business applications with Bonita BPM Community Edition
>>> Quickly connect people, data, and systems into organized workflows
>>> Winner of BOSSIE, CODIE, OW2 and Gartner awards
>>> http://p.sf.net/sfu/Bonitasoft
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Open source business process management suite built on Java and Eclipse
>> Turn processes into business applications with Bonita BPM Community Edition
>> Quickly connect people, data, and systems into organized workflows
>> Winner of BOSSIE, CODIE, OW2 and Gartner awards
>> http://p.sf.net/sfu/Bonitasoft
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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Re: Segments glyph config

Richard Hayes
Yes, subParts should be outside the "style" definitions.

Looks that you have glyph under style, as well, but that's another top-level parameter. Also, the combination of glyph and trackType = CanvasFeatures renders the className definition unnecessary.

Colin, the docs say:
subParts
Comma-separated list of feature type tags that will be drawn as subparts of parent features. Defaults to all features for Segments glyphs, and 'CDS, UTR, five_prime_UTR, three_prime_UTR' for ProcessedTranscript glyphs.

which implies that subParts is not necessary for Segments glyphs, but I've not found that to be true in practice. Perhaps another subtle bug?

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov


On Thu, Jun 26, 2014 at 12:38 PM, Scott Cain <[hidden email]> wrote:
Hi Richard and Colin,

After deleting and recreating the data, deleting cookies and caches (which I don't think I have to do in Chrome with the developer's console is open, right?), and changing the track config to this:

      {
         "style" : {
            "className" : "feature",

            "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
            "glyph" : "JBrowse/View/FeatureGlyph/Segments"
         },
         "subParts" : "exon",

         "key" : "Gene Models (historical)",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
         "compress" : 0,
         "label" : "Gene Models (historical)",
         "type" : "CanvasFeatures",
         "category" : "Not Good"
      },


Nothing changed :-/  Did I not do it right?  I tried subParts both in and out of the style section, but the docs imply that it should be out.

Thanks,
Scott





On Thu, Jun 26, 2014 at 2:43 PM, Richard Hayes <[hidden email]> wrote:
>
> subParts in place of subfeatureClasses was going to be my suggestion. I've found that subParts is nearly always required to tell JBrowse what to render as subfeatures, unless you have a very "standard" GFF3 format as input.
>
> Richard D. Hayes, Ph.D.
> Joint Genome Institute / Lawrence Berkeley National Lab
> http://phytozome.jgi.doe.gov
>
>
> On Thu, Jun 26, 2014 at 11:20 AM, Colin <[hidden email]> wrote:
>>
>> I think you need to set "subParts": "exon" in this track. The style->subfeatureClasses is for HTMLFeatures based rendering. You can see the configuration options here and compare the CanvasFeatures with HTMLFeatures configuration options here http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options
>>
>> -Colin
>>
>>
>> On Thu, Jun 26, 2014 at 1:06 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi All,
>>>
>>> Another day, another "I think I've almost got it" moment.  I'm working on this browser:
>>>
>>> http://dev.wormbase.org:9003/jbrowse/?data=data%2Fc_elegans&loc=X%3A7517701..7603000&tracks=Gene%20Models%20(historical)%2CCurated%20Genes&highlight=
>>>
>>> and I used this command to process data:
>>>
>>> bin/flatfile-to-json.pl \
>>>     --gff ../c_elegans_gff/X.c_elegans.gff3 --out data/c_elegans \
>>>     --type pseudogenic_transcript:history,transposable_element:history,protein_coding_primary_transcript:history,primary_transcript:history,nc_primary_transcript:history \
>>>     --trackLabel "Gene Models (historical)" --trackType CanvasFeatures \
>>>     --key "Gene Models (historical)"
>>>
>>> Note that there are many parent types, none of which are "typical".  The data are pretty straight forward:
>>>
>>> X   history protein_coding_primary_transcript   7551372 7554419 .   -    .       ID=CDS:F46C8.8:wp108;Name=F46C8.8:wp108
>>> X   history exon    7551372 7551463 .   -   .   Parent=CDS:F46C8.8:wp108
>>> X   history exon    7551507 7551674 .   -   .   Parent=CDS:F46C8.8:wp108
>>>
>>> I haven't done much fancy with the config either:
>>>
>>>       {
>>>          "style" : {
>>>             "className" : "feature",
>>>             "glyph" : "JBrowse/View/FeatureGlyph/Segments",
>>>             "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
>>>             "subfeatureClasses" : {
>>>                "exon" : "transcript-CDS"
>>>             },
>>>          },
>>>          "key" : "Gene Models (historical)",
>>>          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
>>>          "trackType" : "CanvasFeatures",
>>>          "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
>>>          "compress" : 0,
>>>          "category" : "Not Good",
>>>          "type" : "CanvasFeatures",
>>>          "label" : "Gene Models (historical)"
>>>       },
>>>
>>> I've tried with and without the subfeatureClasses option, and with transcript-CDS and transcript-exon and several other things as well that didn't work.  What I get is a solid rectangle that represents the extents of the parent feature and I can never get the exons to draw.  Can anybody please point out what I'm doing wrong?
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> Open source business process management suite built on Java and Eclipse
>>> Turn processes into business applications with Bonita BPM Community Edition
>>> Quickly connect people, data, and systems into organized workflows
>>> Winner of BOSSIE, CODIE, OW2 and Gartner awards
>>> http://p.sf.net/sfu/Bonitasoft
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Open source business process management suite built on Java and Eclipse
>> Turn processes into business applications with Bonita BPM Community Edition
>> Quickly connect people, data, and systems into organized workflows
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Turn processes into business applications with Bonita BPM Community Edition
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Re: Segments glyph config

Scott Cain
Hi Richard and Colin,

Moving glyph and subParts out to the top level fixed it, thanks!  Richard, I was going to ask about that documentation piece after you both suggested it but the docs implied it wasn't necessary.  After I got the track working, I removed the subParts option and the track no longer rendered, so I'd say it's a documentation bug (or implementation bug, depending on your point of view).

Scott



On Thu, Jun 26, 2014 at 3:47 PM, Richard Hayes <[hidden email]> wrote:
Yes, subParts should be outside the "style" definitions.

Looks that you have glyph under style, as well, but that's another top-level parameter. Also, the combination of glyph and trackType = CanvasFeatures renders the className definition unnecessary.

Colin, the docs say:
subParts
Comma-separated list of feature type tags that will be drawn as subparts of parent features. Defaults to all features for Segments glyphs, and 'CDS, UTR, five_prime_UTR, three_prime_UTR' for ProcessedTranscript glyphs.

which implies that subParts is not necessary for Segments glyphs, but I've not found that to be true in practice. Perhaps another subtle bug?

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov


On Thu, Jun 26, 2014 at 12:38 PM, Scott Cain <[hidden email]> wrote:
Hi Richard and Colin,

After deleting and recreating the data, deleting cookies and caches (which I don't think I have to do in Chrome with the developer's console is open, right?), and changing the track config to this:

      {
         "style" : {
            "className" : "feature",

            "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
            "glyph" : "JBrowse/View/FeatureGlyph/Segments"
         },
         "subParts" : "exon",

         "key" : "Gene Models (historical)",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
         "compress" : 0,
         "label" : "Gene Models (historical)",
         "type" : "CanvasFeatures",
         "category" : "Not Good"
      },


Nothing changed :-/  Did I not do it right?  I tried subParts both in and out of the style section, but the docs imply that it should be out.

Thanks,
Scott





On Thu, Jun 26, 2014 at 2:43 PM, Richard Hayes <[hidden email]> wrote:
>
> subParts in place of subfeatureClasses was going to be my suggestion. I've found that subParts is nearly always required to tell JBrowse what to render as subfeatures, unless you have a very "standard" GFF3 format as input.
>
> Richard D. Hayes, Ph.D.
> Joint Genome Institute / Lawrence Berkeley National Lab
> http://phytozome.jgi.doe.gov
>
>
> On Thu, Jun 26, 2014 at 11:20 AM, Colin <[hidden email]> wrote:
>>
>> I think you need to set "subParts": "exon" in this track. The style->subfeatureClasses is for HTMLFeatures based rendering. You can see the configuration options here and compare the CanvasFeatures with HTMLFeatures configuration options here http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options
>>
>> -Colin
>>
>>
>> On Thu, Jun 26, 2014 at 1:06 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi All,
>>>
>>> Another day, another "I think I've almost got it" moment.  I'm working on this browser:
>>>
>>> http://dev.wormbase.org:9003/jbrowse/?data=data%2Fc_elegans&loc=X%3A7517701..7603000&tracks=Gene%20Models%20(historical)%2CCurated%20Genes&highlight=
>>>
>>> and I used this command to process data:
>>>
>>> bin/flatfile-to-json.pl \
>>>     --gff ../c_elegans_gff/X.c_elegans.gff3 --out data/c_elegans \
>>>     --type pseudogenic_transcript:history,transposable_element:history,protein_coding_primary_transcript:history,primary_transcript:history,nc_primary_transcript:history \
>>>     --trackLabel "Gene Models (historical)" --trackType CanvasFeatures \
>>>     --key "Gene Models (historical)"
>>>
>>> Note that there are many parent types, none of which are "typical".  The data are pretty straight forward:
>>>
>>> X   history protein_coding_primary_transcript   7551372 7554419 .   -    .       ID=CDS:F46C8.8:wp108;Name=F46C8.8:wp108
>>> X   history exon    7551372 7551463 .   -   .   Parent=CDS:F46C8.8:wp108
>>> X   history exon    7551507 7551674 .   -   .   Parent=CDS:F46C8.8:wp108
>>>
>>> I haven't done much fancy with the config either:
>>>
>>>       {
>>>          "style" : {
>>>             "className" : "feature",
>>>             "glyph" : "JBrowse/View/FeatureGlyph/Segments",
>>>             "color" : "function(f) {var strand = f.get('strand'); if (strand < 0) {return 'violet';} return 'turquoise';  }",
>>>             "subfeatureClasses" : {
>>>                "exon" : "transcript-CDS"
>>>             },
>>>          },
>>>          "key" : "Gene Models (historical)",
>>>          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
>>>          "trackType" : "CanvasFeatures",
>>>          "urlTemplate" : "tracks/Gene Models (historical)/{refseq}/trackData.json",
>>>          "compress" : 0,
>>>          "category" : "Not Good",
>>>          "type" : "CanvasFeatures",
>>>          "label" : "Gene Models (historical)"
>>>       },
>>>
>>> I've tried with and without the subfeatureClasses option, and with transcript-CDS and transcript-exon and several other things as well that didn't work.  What I get is a solid rectangle that represents the extents of the parent feature and I can never get the exons to draw.  Can anybody please point out what I'm doing wrong?
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> Open source business process management suite built on Java and Eclipse
>>> Turn processes into business applications with Bonita BPM Community Edition
>>> Quickly connect people, data, and systems into organized workflows
>>> Winner of BOSSIE, CODIE, OW2 and Gartner awards
>>> http://p.sf.net/sfu/Bonitasoft
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Open source business process management suite built on Java and Eclipse
>> Turn processes into business applications with Bonita BPM Community Edition
>> Quickly connect people, data, and systems into organized workflows
>> Winner of BOSSIE, CODIE, OW2 and Gartner awards
>> http://p.sf.net/sfu/Bonitasoft
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax