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Feature Order of -strand Genes #1071

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nathanhaigh opened this Issue Jun 21, 2018 · 4 comments

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nathanhaigh commented Jun 21, 2018

It seems that the order of features such as exons, CDS etc of genes on the -strand is incorrect from what a user would expect.

A user looking at a gene on the -stand would assume to look at the first CDS feature for an ATG but can't find it. They would have to skip down to the last CDS feature in the list to find the first exon of the gene...this is very confusing.

It would seem that these features are listed in order of 5' -> 3' relative to the reference, not the parent feature. Is there a way to change this behaviour through JBrowse configuration or by modifying information in a GFF3 file?

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cmdcolin commented Jun 21, 2018

This could be nice. Then again a more enhanced gene version of view details would be really good too reference: #174

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nathanhaigh commented Jul 4, 2018

I'd prefer a 2-step resolution to this:

  1. Fix the ordering for complementary strand features
  2. A more gene-centric "view details" page. Some sequence extraction code like https://github.com/tsaari88/FeatureSequence would be useful for people wanting to extract CDS etc.

@rbuels rbuels added this to the 1.15.1 milestone Jul 11, 2018

@rbuels rbuels added the bug label Jul 11, 2018

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rbuels commented Jul 11, 2018

Sounds like the feature sort order in the details view just needs to be reversed if the feature is on the - strand.

And if it doesn't actually do a sort, it should.

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rbuels commented Jul 13, 2018

fixed by merging #1114

@rbuels rbuels closed this Jul 13, 2018

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