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  1. Deep Backlog
  2. DB-103 ProtAnnot Improvements
  3. DB-119

Add labels for gene models and ips result spans

          Details

          • Type: Sub-task
          • Status: Closed (View Workflow)
          • Priority: Major
          • Resolution: Done
          • Labels:
            None

            Attachments

            1. Span1of.PNG
              10 kB
              Mason Meyer
            2. Span1ofProblem.PNG
              11 kB
              Mason Meyer

              Issue Links

              is duplicated by

              Bug - A problem which impairs or prevents the functions of the product. IGBF-850 Some ips matches do not contain entry elements but do have metadata in signature

              • Major - Major loss of function.
              • Closed
              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-898 IPS results spans may be missing complete label information

              • Major - Major loss of function.
              • Closed

                Activity

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                mason Mason Meyer (Inactive) added a comment -

                on 8.4.2 I have found some spans that have labels that are cut off (ex: "Span 1 of").

                To examine this problem you may want to look at a gene id "NM_001144822" under the human genome (Chr1).

                View the attached screenshots to help visualize the problem.

                To reproduce:

                1) Start ProtAnnot for the gene outlined above (NM_001144822).
                2) Run "TMHMM" under InterProScan.

                *Observe:

                Some of the spans (as seen in the screenshots) just say "Span 1 of".

                Show
                mason Mason Meyer (Inactive) added a comment - on 8.4.2 I have found some spans that have labels that are cut off (ex: "Span 1 of"). To examine this problem you may want to look at a gene id "NM_001144822" under the human genome (Chr1). View the attached screenshots to help visualize the problem. To reproduce: 1) Start ProtAnnot for the gene outlined above (NM_001144822). 2) Run "TMHMM" under InterProScan. *Observe: Some of the spans (as seen in the screenshots) just say "Span 1 of".
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                mason Mason Meyer (Inactive) added a comment -

                Also, the labels that are placed into ProtAnnot seem to be invisible during the general workflow of using ProtAnnot. This is probably due to there not being enough space to draw the label but we should examine ways to fix this so these labels are more useful to the user.

                Show
                mason Mason Meyer (Inactive) added a comment - Also, the labels that are placed into ProtAnnot seem to be invisible during the general workflow of using ProtAnnot. This is probably due to there not being enough space to draw the label but we should examine ways to fix this so these labels are more useful to the user.
                Hide
                Permalink
                mason Mason Meyer (Inactive) added a comment -

                Testing for this issue included verifying that PA gene models and IPS result spans contained valid labels. There was a small problem which is being tracked in IGBF-898 but since this issue has been implemented as expected the story will now be closed.

                Show
                mason Mason Meyer (Inactive) added a comment - Testing for this issue included verifying that PA gene models and IPS result spans contained valid labels. There was a small problem which is being tracked in IGBF-898 but since this issue has been implemented as expected the story will now be closed.

                  People

                  • Assignee:
                    mason Mason Meyer (Inactive)
                    Reporter:
                    jeckstein John Eckstein (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: