[Gmod-ajax] Is there support for user defined feature relationships?

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[Gmod-ajax] Is there support for user defined feature relationships?

Chris Childers
Hi all,

I've received a dataset that has non-SO feature types (violating one of the gff3 specifications), and am having a very hard time rendering this properly. Right now the subfeatures are being displayed as separate features on the track, and will not accept any CSS styling. Has anyone run into this issue before? Ideally I would like them to be grouped into one layer, and set the css style.  So doesn't yet have the concept for the 5p and 3p segments of the miRNA, and I'd prefer to keep that information in the underlying data if possible.

Thanks,
Chris

Here are a couple of example features from the file:
Scaffold162       Ma_miR_seeker   gene    6288819 6288893 .       -       .       ID=MIR_LDE_2;NAME=Lde-mir-750-2;
Scaffold162       Ma_miR_seeker   miRNA_pre       6288819 6288893 .       -       .       ID=MIR_PRE_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_pre;
Scaffold162       Ma_miR_seeker   miRNA_5p        6288863 6288888 .       -       .       ID=MIR_MAT_5P_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_5p;
Scaffold162       Ma_miR_seeker   miRNA_3p        6288824 6288849 .       -       .       ID=MIR_MAT_3P_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_3p;
Scaffold162       Ma_miR_seeker   gene    2693239 2693310 .       +       .       ID=MIR_LDE_3;NAME=Lde-mir-317;
Scaffold162       Ma_miR_seeker   miRNA_pre       2693239 2693310 .       +       .       ID=MIR_PRE_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_pre;
Scaffold162     Ma_miR_seeker   miRNA_5p        2693244 2693266 .       +       .       ID=MIR_MAT_5P_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_5p;
Scaffold162       Ma_miR_seeker   miRNA_3p        2693281 2693305 .       +       .       ID=MIR_MAT_3P_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_3p;


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Re: Is there support for user defined feature relationships?

Colin
Hi Chris

One tricky issue is that "PARENT" being capitalized is not valid GFF3 (unfortunately, it is that picky!) so the parent subfeature relationships are not parsed here


If you fix that though, you can get the CanvasFeatures to load those special types with a combination of subParts and the Segments glyph.


      {
         "style" : {
            "className" : "feature"
         },
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "glyph": "JBrowse/View/FeatureGlyph/Segments",
         "urlTemplate" : "tracks/miRNA/{refseq}/trackData.json",
         "label" : "miRNA",
         "subParts" : "miRNA_5p,miRNA_3p"
      }


With HTMLFeatures, you have to generate some custom CSS for each subpart type, or use the subfeatureClasses argument of flatfile-to-json to map the special miRNA type classes to other existing CSS classes (i can elaborate if that helps!)


-Colin




On Tue, Jun 30, 2015 at 10:55 AM, Chris Childers <[hidden email]> wrote:
Hi all,

I've received a dataset that has non-SO feature types (violating one of the gff3 specifications), and am having a very hard time rendering this properly. Right now the subfeatures are being displayed as separate features on the track, and will not accept any CSS styling. Has anyone run into this issue before? Ideally I would like them to be grouped into one layer, and set the css style.  So doesn't yet have the concept for the 5p and 3p segments of the miRNA, and I'd prefer to keep that information in the underlying data if possible.

Thanks,
Chris

Here are a couple of example features from the file:
Scaffold162       Ma_miR_seeker   gene    6288819 6288893 .       -       .       ID=MIR_LDE_2;NAME=Lde-mir-750-2;
Scaffold162       Ma_miR_seeker   miRNA_pre       6288819 6288893 .       -       .       ID=MIR_PRE_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_pre;
Scaffold162       Ma_miR_seeker   miRNA_5p        6288863 6288888 .       -       .       ID=MIR_MAT_5P_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_5p;
Scaffold162       Ma_miR_seeker   miRNA_3p        6288824 6288849 .       -       .       ID=MIR_MAT_3P_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_3p;
Scaffold162       Ma_miR_seeker   gene    2693239 2693310 .       +       .       ID=MIR_LDE_3;NAME=Lde-mir-317;
Scaffold162       Ma_miR_seeker   miRNA_pre       2693239 2693310 .       +       .       ID=MIR_PRE_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_pre;
Scaffold162     Ma_miR_seeker   miRNA_5p        2693244 2693266 .       +       .       ID=MIR_MAT_5P_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_5p;
Scaffold162       Ma_miR_seeker   miRNA_3p        2693281 2693305 .       +       .       ID=MIR_MAT_3P_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_3p;


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GigeNET's Cloud Solutions provide you with the tools and support that
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Re: Is there support for user defined feature relationships?

Chris Childers
I can't believe I missed that PARENT, and also NAME were not in the right case! Fixing that did the trick. 

Thanks!
Chris

On Tue, Jun 30, 2015 at 3:56 PM, Colin <[hidden email]> wrote:
Hi Chris

One tricky issue is that "PARENT" being capitalized is not valid GFF3 (unfortunately, it is that picky!) so the parent subfeature relationships are not parsed here


If you fix that though, you can get the CanvasFeatures to load those special types with a combination of subParts and the Segments glyph.


      {
         "style" : {
            "className" : "feature"
         },
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "glyph": "JBrowse/View/FeatureGlyph/Segments",
         "urlTemplate" : "tracks/miRNA/{refseq}/trackData.json",
         "label" : "miRNA",
         "subParts" : "miRNA_5p,miRNA_3p"
      }


With HTMLFeatures, you have to generate some custom CSS for each subpart type, or use the subfeatureClasses argument of flatfile-to-json to map the special miRNA type classes to other existing CSS classes (i can elaborate if that helps!)


-Colin




On Tue, Jun 30, 2015 at 10:55 AM, Chris Childers <[hidden email]> wrote:
Hi all,

I've received a dataset that has non-SO feature types (violating one of the gff3 specifications), and am having a very hard time rendering this properly. Right now the subfeatures are being displayed as separate features on the track, and will not accept any CSS styling. Has anyone run into this issue before? Ideally I would like them to be grouped into one layer, and set the css style.  So doesn't yet have the concept for the 5p and 3p segments of the miRNA, and I'd prefer to keep that information in the underlying data if possible.

Thanks,
Chris

Here are a couple of example features from the file:
Scaffold162       Ma_miR_seeker   gene    6288819 6288893 .       -       .       ID=MIR_LDE_2;NAME=Lde-mir-750-2;
Scaffold162       Ma_miR_seeker   miRNA_pre       6288819 6288893 .       -       .       ID=MIR_PRE_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_pre;
Scaffold162       Ma_miR_seeker   miRNA_5p        6288863 6288888 .       -       .       ID=MIR_MAT_5P_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_5p;
Scaffold162       Ma_miR_seeker   miRNA_3p        6288824 6288849 .       -       .       ID=MIR_MAT_3P_LDE_2;PARENT=MIR_LDE_2;NAME=Lde-mir-750-2_3p;
Scaffold162       Ma_miR_seeker   gene    2693239 2693310 .       +       .       ID=MIR_LDE_3;NAME=Lde-mir-317;
Scaffold162       Ma_miR_seeker   miRNA_pre       2693239 2693310 .       +       .       ID=MIR_PRE_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_pre;
Scaffold162     Ma_miR_seeker   miRNA_5p        2693244 2693266 .       +       .       ID=MIR_MAT_5P_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_5p;
Scaffold162       Ma_miR_seeker   miRNA_3p        2693281 2693305 .       +       .       ID=MIR_MAT_3P_LDE_3;PARENT=MIR_LDE_3;NAME=Lde-mir-317_3p;


------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
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https://www.gigenetcloud.com/
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