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  1. IGB
  2. IGBF-3489

Tweaking the EBSEQ to merge results into a master table

        Details

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

          Description

          As it currently stands, The EBseq r script produces 6 result files.
          I stitch these together using a python script into 1 master table.

          It will be smoother overall to have this happen from within the EBSEQ script instead.

          Goal: Is to add a few steps to existing EBseq script to make a master table of all the results.

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              Task - A task that needs to be done. IGBF-3477 EBSEQ: The bigger table version

              • 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-3477 [ IGBF-3477 ]
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-2993 [ 21429 ] IGBF-3446 [ 22548 ]
                robofjoy Robert Reid made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Robert Reid [ robertreid ] Molly Davis [ molly ]
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                Mdavis4290 Molly Davis added a comment - - edited

                Script: Ebseq-hmm_mudayTimeCourse-Version3.R

                I have updated the script so that it works in the flavonoid repo and am now reviewing output files.

                Show
                Mdavis4290 Molly Davis added a comment - - edited Script : Ebseq-hmm_mudayTimeCourse-Version3.R I have updated the script so that it works in the flavonoid repo and am now reviewing output files.
                Mdavis4290 Molly Davis made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                Mdavis4290 Molly Davis added a comment - - edited

                Branch: https://bitbucket.org/mdavis4290/molly4-flavonoid-rnaseq/branch/IGBF-3489

                Notes: I created a new folder in 72_F3H_PollenTube directory called EBseq. This folder contains the R script that Dr. Reid wrote and all of the output files from the script.

                Show
                Mdavis4290 Molly Davis added a comment - - edited Branch : https://bitbucket.org/mdavis4290/molly4-flavonoid-rnaseq/branch/IGBF-3489 Notes: I created a new folder in 72_F3H_PollenTube directory called EBseq. This folder contains the R script that Dr. Reid wrote and all of the output files from the script.
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                Mdavis4290 Molly Davis made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
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                Mdavis4290 Molly Davis added a comment -

                PR: https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/36

                Show
                Mdavis4290 Molly Davis added a comment - PR : https://bitbucket.org/hotpollen/flavonoid-rnaseq/pull-requests/36
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5 [ 181 ] Fall 5, Fall 6 [ 181, 182 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
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                ann.loraine Ann Loraine added a comment -

                Nice approach for organizing the code and results. Thanks [~molly] and [~RobertReid]! This makes it very easy to read and understand the work!

                Show
                ann.loraine Ann Loraine added a comment - Nice approach for organizing the code and results. Thanks [~molly] and [~RobertReid] ! This makes it very easy to read and understand the work!
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                Merged and moved to "ready for testing."

                I would recommend that [~RobertReid] take a look to check that everything required to understand and also to reproduce the results is there.

                Show
                ann.loraine Ann Loraine added a comment - Merged and moved to "ready for testing." I would recommend that [~RobertReid] take a look to check that everything required to understand and also to reproduce the results is there.
                Mdavis4290 Molly Davis made changes -
                Assignee Robert Reid [ robertreid ]
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                robofjoy Robert Reid added a comment -

                I have downloaded from the repo.

                I opened the R script and ran it.
                The 7 expected results files are there.
                The fill table looks correct when opened in Excel.

                I say this is ready to be closed.

                Show
                robofjoy Robert Reid added a comment - I have downloaded from the repo. I opened the R script and ran it. The 7 expected results files are there. The fill table looks correct when opened in Excel. I say this is ready to be closed.
                robofjoy Robert Reid made changes -
                Assignee Robert Reid [ robertreid ] Molly Davis [ molly ]
                robofjoy Robert Reid made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Robert Reid [ robertreid ]
                Mdavis4290 Molly Davis made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
                  • Votes:
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: