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  1. IGB
  2. IGBF-2123

Investigate: Re-design and update Transcript isoform App

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      4
    • Sprint:
      Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun

      Description

      When we first started migrating to OSGi, developer Lance Frohman (Genentech) created a plug-in that drew a sashimi-plot graphic on top of gene models to highlight splicing support.

      Recently, we moved the code to a new repository:

      https://bitbucket.org/lorainelab/development-apps/src/master/TranscriptIsoform/

      Let's revisit this code and investigate what it would be take to implement it now.

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            Hide
            prutha Prutha Kulkarni (Inactive) added a comment -

            Sure. I will do that asap

            Show
            prutha Prutha Kulkarni (Inactive) added a comment - Sure. I will do that asap
            Show
            prutha Prutha Kulkarni (Inactive) added a comment - PR submitted. code changes can be found at: https://bitbucket.org/lorainelab/experimental-apps-for-igb/pull-requests/12/igbf-2123-refactor-transcriptisoform-app/diff
            Hide
            ann.loraine Ann Loraine added a comment -

            PR merged.

            • commit: IGBF-2123 : Refactor TranscriptIsoform App

            is now on master branch.

            cc: Prutha Kulkarni

            Show
            ann.loraine Ann Loraine added a comment - PR merged. commit: IGBF-2123 : Refactor TranscriptIsoform App is now on master branch. cc: Prutha Kulkarni
            Hide
            ann.loraine Ann Loraine added a comment -

            Note this cannot be tested until the bitbucket pipelines are configured properly at the team repository at https://bitbucket.org/lorainelab/transcriptisoform. Hence IGBF-2373 is a blocker for testing.

            Show
            ann.loraine Ann Loraine added a comment - Note this cannot be tested until the bitbucket pipelines are configured properly at the team repository at https://bitbucket.org/lorainelab/transcriptisoform . Hence IGBF-2373 is a blocker for testing.
            Hide
            pbadzuh Philip Badzuh (Inactive) added a comment - - edited

            Tested on the latest dev version of IGB on macOS.

            • The expected behavior described in this comment occurs.
            • Toggling between the View > Transcript Isoform > Show density options results in visually different 'chevrons' in the intergenic reference tiers. I am not sure of the significance of these differences or what they are expected to be, but the functionality of the app from the new repo seems to resemble that of the same app from the experimental apps repo.
            • I noticed that the build at the new repo fails, but since IGBF-2373 has been resolved, it may be good to try the build again.
            • Some intergenic regions have multiple overlapping 'chevrons' on the reference tiers. Is this expected? I have attached a screenshot (overlapping_chevrons.png) - the same behavior seems to be present when running the app from the experimental repo.

            The app seems to be functioning as expected. Moving to done.

            Show
            pbadzuh Philip Badzuh (Inactive) added a comment - - edited Tested on the latest dev version of IGB on macOS. The expected behavior described in this comment occurs. Toggling between the View > Transcript Isoform > Show density options results in visually different 'chevrons' in the intergenic reference tiers. I am not sure of the significance of these differences or what they are expected to be, but the functionality of the app from the new repo seems to resemble that of the same app from the experimental apps repo. I noticed that the build at the new repo fails, but since IGBF-2373 has been resolved, it may be good to try the build again. Some intergenic regions have multiple overlapping 'chevrons' on the reference tiers. Is this expected? I have attached a screenshot (overlapping_chevrons.png) - the same behavior seems to be present when running the app from the experimental repo. The app seems to be functioning as expected. Moving to done.

              People

              • Assignee:
                Unassigned
                Reporter:
                ann.loraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: