Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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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 2
Description
The list of Restriction Enzymes currently in IGB could use some updating. Please see the attachment for a list of RE's that need to be added. Do note that there's a second tab with RE's that may be a bit outdated but are still listed in IGB.
Attachments
Issue Links
- relates to
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IGBF-3554 Investigate error with mapping restriction enzymes over whole chromosome
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Rank | Ranked higher |
| Epic Link | IGBF-1765 [ 17855 ] |
| Story Points | 1 |
| Story Points | 1 | 2 |
| Sprint | Spring 2 [ 186 ] | |
| Assignee | Kaushik Gopu [ kgopu ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Hide
Kaushik Gopu
added a comment - - edited
Permalink
- Updated a file with new restricting enzymes.
- Some enzymes contain special nucleotide symbols such as N, Y, and R. The IGB plugin, RestrictionSites, is not processing these symbols.
- This situation is similar to IGBF-3236.
Show
Kaushik Gopu
added a comment - - edited
Updated a file with new restricting enzymes.
Some enzymes contain special nucleotide symbols such as N, Y, and R. The IGB plugin, RestrictionSites , is not processing these symbols.
This situation is similar to IGBF-3236 .
| Attachment | Restriction Enzymes - Clean.xlsx [ 18186 ] |
| Attachment | rest_enzymes [ 18187 ] |
| Attachment | Restriction Enzymes - Ready for IGB.xlsx [ 18188 ] |
- Updated rest_enzymes file with new restriction enzymes (in sorted order)
- Added support to process special nucleotides
- Build and run this branch.
- Test enzymes that have special nucleotides such as M, K, R, etc. (AccI->GTMKAC, AflIII->ACRYGT)
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Kaushik Gopu [ kgopu ] |
| Attachment | rest_enzymes [ 18187 ] |
| Attachment | Restriction Enzymes - Clean.xlsx [ 18186 ] |
| Attachment | rest_enzymes [ 18190 ] |
Tested on Mac, working correctly.
Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/984
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Ann Loraine [ aloraine ] |
PR is merged and installers are built. Ready for testing.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Comment | [ PR is merged and installers are built. Ready for testing. ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Tested using IGB-macos-universal-main-JDK21-with-javafx-no-theme.dmg installer on Mac.
Working correctly, closing ticket.
| Assignee | Nowlan Freese [ nfreese ] | Kaushik Gopu [ kgopu ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 10.0.0 Major Release [ 10900 ] |
| Issue Type | Task [ 3 ] | Improvement [ 4 ] |