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  1. IGB
  2. IGBF-3229

Complete gene description transfer

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Blocker
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Follow up on IGBF-3145 (linked):

          • Modify the output file format to not wrap any of the fields with quotation marks.
          • Modify the code chunk to no longer print out an entire data frame to the final knitted document
          • Ensure that the file can "knit" without error
          • Create output file in a subdirectory named "output" or whatever.
          • Add knitted output (e.g., .html file, but nothing else) to repository, same location as corresponding .Rmd file.
          • Ensure that IGB can open the file (investigate command-line options for IGB to speed up development and automate testing)

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3145 Transfer SL4.0 gene descriptions to SL5.0 annotations

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3145 [ IGBF-3145 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                ann.loraine Ann Loraine added a comment - - edited

                Mapping file contains what look like redundancies and inconsistencies.
                Modifying the Markdown to investigate.

                Show
                ann.loraine Ann Loraine added a comment - - edited Mapping file contains what look like redundancies and inconsistencies. Modifying the Markdown to investigate.
                ann.loraine Ann Loraine made changes -
                Sprint Fall 7 2022 Nov 21 [ 159 ] Fall 7 2022 Nov 21, Fall 8 2022 Dec 5 [ 159, 160 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                ann.loraine Ann Loraine added a comment -

                Opened the new BED-detail file in IGB and found a problem.

                One of the genes Solyc01G001683 has multiple gene models, only two of which got a description and all the rest still are "NA". Investigating.

                Show
                ann.loraine Ann Loraine added a comment - Opened the new BED-detail file in IGB and found a problem. One of the genes Solyc01G001683 has multiple gene models, only two of which got a description and all the rest still are "NA". Investigating.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Fixed it. Was using a conventional assignment operator inside a function that was getting used in an "sapply" call. Changed it to "<<-" to ensure that the assignment would affect the enclosing frame and therefore persist after the function returned.

                Viewed the file in IGB and it seemed OK. Did not check the functional assignments however.

                Show
                ann.loraine Ann Loraine added a comment - Fixed it. Was using a conventional assignment operator inside a function that was getting used in an "sapply" call. Changed it to "<<-" to ensure that the assignment would affect the enclosing frame and therefore persist after the function returned. Viewed the file in IGB and it seemed OK. Did not check the functional assignments however.
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

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

                    • Created:
                      Updated:
                      Resolved: