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fixes #2565 - removes featureLocationPublications#2573

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nathandunn merged 14 commits into
developfrom
fix-2565-partials
Feb 16, 2021
Merged

fixes #2565 - removes featureLocationPublications#2573
nathandunn merged 14 commits into
developfrom
fix-2565-partials

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@nathandunn

@nathandunn nathandunn commented Feb 12, 2021

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fixes #2565
fixes #2574

  • remove feature location publications
  • create service and use specific REST to access it
  • add to UI (in location region)
  • service should set all child elements if they share a boundary as well
  • output to GFF3
  • extend to transcript panel

  • add "isObselete" to interface in detail
    • add "showObsolete" to features in AnnotatorPanel
  • should use updateFeature
  • update from server
  • double-check the export for GFF3
  • extend to transcript panel (can be done individually)

  • update changelog

@nathandunn

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@uliboehme I have some questions about obsolete / and partials

  • how do you export obsolete and partials in the GFF3?
  • can you obsolete a transcript by itself (without the gene?) or is it always the entire gene model?
  • when setting a partial for a gene, I'm assuming that any aligning Transcript / Exon / CDS might also pick up the partial?

@uliboehme

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@nathandunn

  • Partials genes are shown in the GFF file with
    start_range=.,.
    end_range=.,.
    I have not exported obsolete genes.

  • You can obsolete a transcript by itself. I've used this option for genes with alternative transcripts.

  • You are right, when setting a partial for a gene, transcript, exon, CDS are also picking up the partial.

@nathandunn
nathandunn merged commit 8149e2a into develop Feb 16, 2021
@cmdcolin
cmdcolin deleted the fix-2565-partials branch December 7, 2023 20:05
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allow obsolete to be set Option to mark a gene as partial in Apollo

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