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: 10.1.0
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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
Description
Develop code to connect to this https://api.genome.ucsc.edu/getData/track?genome=hg38&track=encTfChipPkENCFF865QLX&chrom=chr1&start=1&end=2480000 API and load Data for the narrowPeak file type. Investigate the existing file type and add logic to parse the narrowPeak file format.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
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| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 5 [ 189 ] | Spring 5, Spring 6 [ 189, 190 ] |
| Rank | Ranked higher |
| Attachment | Screenshot 2024-03-22 at 1.22.40 PM.png [ 18294 ] |
Code changes are completed to include the narrowPeak file type as well in the supported file types for UCSC and added logic to parse them. Written test case for the same. Updated code is available at the branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3657.
To test:
- Download https://bitbucket.org/jaya-sravani/integrated-genome-browser/downloads/ installer or clone this branch to local https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3657 and start the application.
- Select a particular genome. (note: hg38 has data for this track)
- Select any narrowPeak track (dataset) type.
- Click on the load data button either from the top right corner or in the data management table.
- Check whether the data is loaded correctly and the peak is visible.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Tested using file downloaded from UCSC table browser (encTfChipPkENCFF635MUK.narrowPeak) and comparing to the same file as loaded through UCSC REST API (encTfChipPkENCFF635MUK).
Also compared to the following REST call: https://api.genome.ucsc.edu/getData/track?genome=hg38&track=encTfChipPkENCFF635MUK&chrom=chr1&start=1615401&end=1616106
Files loaded in IGB appeared identical and matched with the REST call.
Ready for pull request.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Attachment | encTfChipPkENCFF635MUK.narrowPeak.gz [ 18299 ] |
Raised a Pull Request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/993. Please review and let me know if there are any issues.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
Merged.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Sprint | Spring 5, Spring 6 [ 189, 190 ] | Spring 5, Spring 6, Spring 7 [ 189, 190, 191 ] |
| Rank | Ranked higher |
New PR is merged. New "early access" installers are built and deployed to BioViz.org.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Tested using the main branch from loraine lab. Used the same testing strategy outlined in my previous comment.
Files loaded in IGB appeared identical and matched with the REST call.
Closing ticket.
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 10.1.0 [ 11000 ] |
Use logic in the parseLineToDataModel method in NarrowPeak Symloader class to create parsing logic for narrowPeak file type in the UCSC Rest API module.