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 4, Spring 5
Description
Situation: The UCSC REST endpoint provides many more track types than DAS. Some of them can be easily mapped to IGB's bed parser or a graph parser, but others we are unsure of.
Task: List out the different track types being provided by UCSC REST and determine which tracks can be easily parsed by IGB.
Attachments
Issue Links
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
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- Example URL discussing the schema for repeatmasker: https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=rmsk
- API schema for alligator track netGalGal6 https://api.genome.ucsc.edu/list/schema?genome=allMis1;track=netGalGal6
- Data types found in tracks: http://genome.ucsc.edu/FAQ/FAQformat.html
- IGB File Formats: https://wiki.bioviz.org/confluence/display/igbman/File+Formats#:~:text=IGB%20supports%20partial%20data%20loading,indexed%20file%20and%20its%20index%20(.
Google sheet link with track types and whether (I think) we can parse them in IGB: https://docs.google.com/spreadsheets/d/1epLMB2zPOjReiJ9L7-UcX8gCn52yIoquc4ufUrH0uS0/edit?usp=sharing
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 4 [ 188 ] | Spring 4, Spring 5 [ 188, 189 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Looking into the file types mentioned in the above spreadsheet, investing a way on how to parse it, searching if there's any existing logic in code that might support it, and making notes on the findings.
After discussion with Sravani we have decided the following.
Create new tickets implementing:
- narrowPeak > parse as narrowPeak
- bigGenePred > parse as either bed or genePred
- barChart > parse as bed or graph
The following formats will require additional investigation, but we will not implement them as part of this epic:
- chain
- net
- rmsk
- wigMaf
Created tickets for the three file types (narrowPeak, bigGenePred, and barChart). Closing this ticket now and will start working on these tickets.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| 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 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |