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  1. IGB
  2. IGBF-4223

Make table of Gene lengths

        Details

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

          Description

          Take SL4 CDS file and create a new table that contains just 2 columns

          The SOLYID
          The gene length

          Read in each fasta, Calculate the length of the sequence.

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              Issue Links

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              Task - A task that needs to be done. IGBF-4220 Normalize Salmon Counts

              • Major - Major loss of function.
              • Closed

                Activity

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                robofjoy Robert Reid created issue -
                robofjoy Robert Reid made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                robofjoy Robert Reid made changes -
                Link This issue blocks IGBF-4220 [ IGBF-4220 ]
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                bbendick Brandon Bendickson made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                bbendick Brandon Bendickson made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                bbendick Brandon Bendickson made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                bbendick Brandon Bendickson made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                bbendick Brandon Bendickson made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                bbendick Brandon Bendickson made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                bbendick Brandon Bendickson made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                bbendick Brandon Bendickson made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                robofjoy Robert Reid made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                robofjoy Robert Reid added a comment -

                The table produces decimal points.
                Many of them.
                Like a boat load.
                Too many.

                Can we add a step prior to writing to file to floor each number in table to 2 decimal points ?

                The reason is I am getting a

                Error: vector memory limit of 32.0 Gb reached, see mem.maxVSize()

                I bet the decimals are the cause.

                Show
                robofjoy Robert Reid added a comment - The table produces decimal points. Many of them. Like a boat load. Too many. Can we add a step prior to writing to file to floor each number in table to 2 decimal points ? The reason is I am getting a Error: vector memory limit of 32.0 Gb reached, see mem.maxVSize() I bet the decimals are the cause.
                robofjoy Robert Reid made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                robofjoy Robert Reid made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                robofjoy Robert Reid made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                robofjoy Robert Reid made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                robofjoy Robert Reid made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                robofjoy Robert Reid made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                Decimals were not the cause.
                Rob's Rstudio no like it, specifically spmething about tidyverse.

                When I read it using read.delim, all is well.

                So this table is not the issue.

                Show
                robofjoy Robert Reid added a comment - Decimals were not the cause. Rob's Rstudio no like it, specifically spmething about tidyverse. When I read it using read.delim, all is well. So this table is not the issue.

                  People

                  • Assignee:
                    bbendick Brandon Bendickson
                    Reporter:
                    robofjoy Robert Reid
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                    Dates

                    • Created:
                      Updated:
                      Resolved: