Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 5, Spring 6, Spring 7, Spring 8, Spring 9
Description
mark-2022-timeseries experiment has been submitted to SRA and rerun with nextflow. A sanity check will need to be performed on the original data and the rerun SRA data to ensure the submission to NCBI was correct.
The next step is adding the SRA data to IGB Quickload. To do this a sample sheet is required.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] | Ann Loraine [ aloraine ] |
| Sprint | Spring 5 [ 189 ] | Spring 5, Spring 6 [ 189, 190 ] |
| Rank | Ranked higher |
| Sprint | Spring 5, Spring 6 [ 189, 190 ] | Spring 5, Spring 6, Spring 7 [ 189, 190, 191 ] |
| Rank | Ranked higher |
Please check with makeAnnotsXml.py for the next step.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Adding SRA submission to makeAnnotsXml.py
# Johnson lab mark-2022-timeseries SRA submission SRP441343
repo = "https://bitbucket.org/hotpollen/splicing-analysis"
branch = "main"
filename = "SRP441343_sample_sheet.xlsx"
path = "ExternalData/"+filename
getSampleSheetFromRepo(filename,repo,path,branch)
spreadsheet = pd.read_excel(filename)
sample_sheet = SampleSheet(spreadsheet)
sample_sheet.addGenome(SL5)
sample_sheet.addGenome(SL4)
to_return.append(sample_sheet)
export PYTHONPATH=/Users/mollydavis333/Desktop/igbquickload
python -m pip install requests
pip install openpyxl
conda create -c conda-forge -n name_of_my_env python pandas
source activate name_of_my_env
./makeAnnotsXml.py
| Summary | Make sample sheet for SRP441343 | Make sample sheet for SRP441343 and add to makeAnnotsXml.py |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 5, Spring 6, Spring 7 [ 189, 190, 191 ] | Spring 5, Spring 6, Spring 7, Spring 8 [ 189, 190, 191, 192 ] |
| Rank | Ranked higher |
I did not try to run the new code as Molly Davis has already been able to run it, as noted above.
Moving to "ready for pull request."
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Assignee | Molly Davis [ molly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
PR is merged. Ready for testing.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 5, Spring 6, Spring 7, Spring 8 [ 189, 190, 191, 192 ] | Spring 5, Spring 6, Spring 7, Spring 8, Spring 9 [ 189, 190, 191, 192, 193 ] |
| Rank | Ranked higher |
Sample sheet is good. Moving to DONE.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Molly Davis [ molly ] |
Branch: https://bitbucket.org/mdavis4290/molly-2-splicing-analysis/branch/IGBF-3638b