Uploaded image for project: 'Deep Backlog'
  1. Deep Backlog
  2. DB-146

Incorrect parsing of multiline GFF3 files

          Details

          • Type: Bug
          • Status: Open (View Workflow)
          • Priority: Major
          • Resolution: Unresolved
          • Labels:
            None

            Description

            A user had an issue with a .gff3 file not showing up correctly in IGB (https://jira.transvar.org/browse/HELP-101). The issue appears to stem from IGB incorrectly parsing multiline .gff3 files. For example, compare how IGB loads the attached .bed and .gff3, both generated from the same data and following the accepted formats. In the .gff3 file, only the first line of a gene is displayed, while the rest are ignored.

              Attachments

              1. closeup of gff3 parents.PNG
                closeup of gff3 parents.PNG
                73 kB
              2. Parent GlyphsShown.PNG
                Parent GlyphsShown.PNG
                80 kB
              3. Sample.bed
                1 kB
              4. Sample.gff3
                4 kB

                Activity

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-439 [ 15497 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Assignee David Norris [ dcnorris ]
                Hide
                Permalink
                mason Mason Meyer (Inactive) added a comment -

                I also noticed that the GFF3 file may display the parent glyphs as well as the chldren (see attached screenshots).

                Show
                mason Mason Meyer (Inactive) added a comment - I also noticed that the GFF3 file may display the parent glyphs as well as the chldren (see attached screenshots).
                mason Mason Meyer (Inactive) made changes -
                Attachment closeup of gff3 parents.PNG [ 13014 ]
                Attachment Parent GlyphsShown.PNG [ 13015 ]
                ann.loraine Ann Loraine made changes -
                Project IGB [ 10840 ] Deep Backlog [ 11041 ]
                Key IGBF-518 DB-146
                Workflow Loraine Lab Workflow [ 15784 ] jira [ 16853 ]
                ann.loraine Ann Loraine made changes -
                Story Points 0.5

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated: