[IGBF-3338] Add and test KP 2023 sample sheet data to "hotpollen" annots.xml - JIRA UNCC

Details

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

Story Points:
0.5
Epic Link:
Process and deploy Palanivelu Lab data
Sprint:
Summer 1 2023 May 15

Description

Directory: ../genome-browser-visualization/makeAnnotsXml.py

def readSpreadsheet5(fname="../pistil-rna-seq/ExternalData/KP_sample_sheet.xlsx"):
    if fname:
        return pd.read_excel(fname)
    else:
        repo = "https://bitbucket.org/hotpollen/pistil-rna-seq"
        branch = "main"
        filename = "KP_sample_sheet.xlsx"
        path = "ExternalDataSets/"+filename
        getSampleSheetFromRepo(filename,repo,path,branch)
        return pd.read_excel(filename)

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Issue Links

relates to

IGBF-3326 Create KP 2023 sample sheet needed for Quickload site and more

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Activity

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Molly Davis added a comment - 18/May/23 11:03 AM

Branch: https://bitbucket.org/mdavis4290/molly-genome-browser-visualization/branch/IGBF-3338
Pull Request: https://bitbucket.org/hotpollen/genome-browser-visualization/pull-requests/2

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Molly Davis added a comment - 18/May/23 11:03 AM Branch : https://bitbucket.org/mdavis4290/molly-genome-browser-visualization/branch/IGBF-3338 Pull Request : https://bitbucket.org/hotpollen/genome-browser-visualization/pull-requests/2

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Ann Loraine added a comment - 19/May/23 9:21 AM

PR is merged. Note sure where to move this ticket next since currently "in progress"

[~molly] please advise.

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Ann Loraine added a comment - 19/May/23 9:21 AM PR is merged. Note sure where to move this ticket next since currently "in progress" [~molly] please advise.

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Ann Loraine added a comment - 19/May/23 10:10 AM - edited

To test:

Run the makeAnnotsXml.py script on your local. This will create a new "annots.xml" file on your local. The annots.xml file controls what users see for that quickload site in the data access panel.
Use IGB to open the resulting quickload site on your local.
Check visually how the data appear in the IGB Data Access panel
Click on all the items to ensure they can load into IGB
If the data set names are not intuitive or the colors look bad (e.g., light colors on white background are not great), make a change to the spreadsheet

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Ann Loraine added a comment - 19/May/23 10:10 AM - edited To test: Run the makeAnnotsXml.py script on your local. This will create a new "annots.xml" file on your local. The annots.xml file controls what users see for that quickload site in the data access panel. Use IGB to open the resulting quickload site on your local. Check visually how the data appear in the IGB Data Access panel Click on all the items to ensure they can load into IGB If the data set names are not intuitive or the colors look bad (e.g., light colors on white background are not great), make a change to the spreadsheet

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Molly Davis added a comment - 19/May/23 11:25 AM - edited

IGB Testing:
How to test: https://wiki.bioviz.org/confluence/display/igbman/Adding+and+Managing+Data+Source+Servers

I was able to configure a local quick load and view the data in IGB. There was an issue with the unpollinated file names in the KP_sample_sheet.csv and quick load site (http://lorainelab-quickload.scidas.org/hotpollen/S_lycopersicum_Jun_2022/pistil/) :

Heinz-Rep1-0hr-25C-unpol -> Heinz-Ovary-Rep1-0hr-25C-unpol

Heinz-Rep2-0hr-25C-unpol -> Heinz-Ovary-Rep2-0hr-25C-unpol

Heinz-Rep3-0hr-25C-unpol -> Heinz-Ovary-Rep3-0hr-25C-unpol

Fix: change the names in the sample sheet to include 'Ovary', and then the links should start working for IGB. The rest of the files do load in IGB and seem to be visually correct.

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Molly Davis added a comment - 19/May/23 11:25 AM - edited IGB Testing : How to test: https://wiki.bioviz.org/confluence/display/igbman/Adding+and+Managing+Data+Source+Servers I was able to configure a local quick load and view the data in IGB. There was an issue with the unpollinated file names in the KP_sample_sheet.csv and quick load site ( http://lorainelab-quickload.scidas.org/hotpollen/S_lycopersicum_Jun_2022/pistil/ ) : Heinz-Rep1-0hr-25C-unpol -> Heinz-Ovary-Rep1-0hr-25C-unpol Heinz-Rep2-0hr-25C-unpol -> Heinz-Ovary-Rep2-0hr-25C-unpol Heinz-Rep3-0hr-25C-unpol -> Heinz-Ovary-Rep3-0hr-25C-unpol Fix : change the names in the sample sheet to include 'Ovary', and then the links should start working for IGB. The rest of the files do load in IGB and seem to be visually correct.

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Molly Davis added a comment - 19/May/23 11:44 AM - edited

Fix for KP_sample_sheet.xlsx:

Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3338b
Pull Request: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/4

Next Step: Once the sample sheet is updated rerun makeAnnotsXml.py script on local machine and check annots.xml file in IGB to ensure the URL's are working now. If working should I commit new changes for annots.xml to bitbucket?

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Molly Davis added a comment - 19/May/23 11:44 AM - edited Fix for KP_sample_sheet.xlsx : Branch : https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3338b Pull Request : https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/4 Next Step: Once the sample sheet is updated rerun makeAnnotsXml.py script on local machine and check annots.xml file in IGB to ensure the URL's are working now. If working should I commit new changes for annots.xml to bitbucket?

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Ann Loraine added a comment - 22/May/23 10:38 AM

PR is merged.

attn: [~molly]

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Ann Loraine added a comment - 22/May/23 10:38 AM PR is merged. attn: [~molly]

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Molly Davis added a comment - 22/May/23 11:27 AM - edited

Updated and tested annots.xml in IGB:

Branch: https://bitbucket.org/mdavis4290/molly-genome-browser-visualization/branch/IGBF-3338b
Pull Request: https://bitbucket.org/hotpollen/genome-browser-visualization/pull-requests/3

attn: [~aloraine]

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Molly Davis added a comment - 22/May/23 11:27 AM - edited Updated and tested annots.xml in IGB : Branch : https://bitbucket.org/mdavis4290/molly-genome-browser-visualization/branch/IGBF-3338b Pull Request : https://bitbucket.org/hotpollen/genome-browser-visualization/pull-requests/3 attn: [~aloraine]

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Ann Loraine added a comment - 25/May/23 10:17 AM

Everything merged and ready for testing.

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Ann Loraine added a comment - 25/May/23 10:17 AM Everything merged and ready for testing.

People

Assignee:

Unassigned

Reporter:

Molly Davis

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Watchers:

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Dates

Created:

15/May/23 10:20 AM

Updated:

27/Jul/23 4:33 PM

Resolved:

25/May/23 10:17 AM