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  1. IGB
  2. IGBF-1092

Save As... (bedgraph) feature uses spaces instead of tabs

        Details

        • Story Points:
          3
        • Sprint:
          Fall 2017

          Description

          It seems that the Save As... feature is exporting bedgraph files using spaces instead of tabs, so this should be fixed.

          We should also check to see if other formats are being exported using spaces instead of tabs.

          Also, change the comment line to show the genome version instead of chromosome name.

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              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1128 Save As... feature appends extra text that can cause the file name to be invalid

              • Major - Major loss of function.
              • Closed

                Activity

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                mason Mason Meyer (Inactive) created issue -
                mason Mason Meyer (Inactive) made changes -
                Field Original Value New Value
                Rank Ranked higher
                mason Mason Meyer (Inactive) made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Sprint 39 [ 47 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Story Points 0.5
                Resolution Unresolved [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Assignee Devdatta Kulkarni [ deva ]
                mason Mason Meyer (Inactive) made changes -
                Resolution Unresolved [ 10101 ]
                Status Open [ 1 ] Open [ 1 ]
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                ann.loraine Ann Loraine added a comment -

                A bedgraph file is a file format for representing "genome graphs"

                Genome graphs are data types where bases (letters) in the sequence axis are associated with numeric values.

                To see one, do this:

                • Select Arabidopsis thaliana genome - go to start screen and click the Arabidopsis image
                • Choose Data Access > RNA-Seq > Loraine Lab > Mixed Cold > SM > Graph
                • Select a graph, zoom in on a region
                • Click Load Data to load some data
                • Right-click or CNTRL-click track label and select Save As...
                Show
                ann.loraine Ann Loraine added a comment - A bedgraph file is a file format for representing "genome graphs" Genome graphs are data types where bases (letters) in the sequence axis are associated with numeric values. To see one, do this: Select Arabidopsis thaliana genome - go to start screen and click the Arabidopsis image Choose Data Access > RNA-Seq > Loraine Lab > Mixed Cold > SM > Graph Select a graph, zoom in on a region Click Load Data to load some data Right-click or CNTRL-click track label and select Save As...
                ann.loraine Ann Loraine made changes -
                Description It seems that the Save As... feature is exporting bedgraph files using spaces instead of tabs, so this should be fixed.

                We should also check to see if other formats are being exported using spaces instead of tabs.                 		It seems that the Save As... feature is exporting bedgraph files using spaces instead of tabs, so this should be fixed.

                We should also check to see if other formats are being exported using spaces instead of tabs.

                Also, change the comment line to show the genome version instead of chromosome name.
                deva Devdatta Kulkarni (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                deva Devdatta Kulkarni (Inactive) made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Story Points 0.5 3
                Assignee Devdatta Kulkarni [ deva ] Jennifer Daly [ jdaly ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                mason Mason Meyer (Inactive) made changes -
                Fix Version/s 9.0.1 Minor Release [ 10500 ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Status In Progress [ 3 ] Needs Testing [ 10002 ]
                mason Mason Meyer (Inactive) made changes -
                Link This issue relates to IGBF-1128 [ IGBF-1128 ]
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                mason Mason Meyer (Inactive) added a comment - - edited

                My testing of this issue confirms that it is resolved. Using the Save As...(bedgraph) feature now saves a bedgraph file properly, using tabs instead of spaces. Also, the comment line now shows the genome version name instead of the chromosome name, as expected. Since this issue is resolved, it will now be closed, but I am creating IGBF-1128 to track a related issue that was present before this fix was put in place. It seems that the Save As... feature is not usable on Windows because extra text gets appended to the filename, causing the filename to be invalid. See IGBF-1128 for more details.

                Show
                mason Mason Meyer (Inactive) added a comment - - edited My testing of this issue confirms that it is resolved. Using the Save As...(bedgraph) feature now saves a bedgraph file properly, using tabs instead of spaces. Also, the comment line now shows the genome version name instead of the chromosome name, as expected. Since this issue is resolved, it will now be closed, but I am creating IGBF-1128 to track a related issue that was present before this fix was put in place. It seems that the Save As... feature is not usable on Windows because extra text gets appended to the filename, causing the filename to be invalid. See IGBF-1128 for more details.
                mason Mason Meyer (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Needs Testing [ 10002 ] Closed [ 6 ]
                mason Mason Meyer (Inactive) made changes -
                Assignee Jennifer Daly [ jdaly ] Mason Meyer [ mason ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 16973 ] Fall 2019 Workflow Update [ 19761 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19761 ] Revised Fall 2019 Workflow Update [ 21880 ]

                  People

                  • Assignee:
                    mason Mason Meyer (Inactive)
                    Reporter:
                    mason Mason Meyer (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: