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:4
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Epic Link:
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Sprint:Fall 7, Fall 8, Spring 1, Spring 2, Spring 3, Spring 4
Description
Develop code to connect to this https://api.genome.ucsc.edu//getData/track?genome=hg38&track=ReMapDensity&chrom=chr1&start=1&end=248956 API and load Data for the Wiggle file type.
Attachments
Issue Links
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- Closed
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Activity
| Description | Develop code to connect to this https://api.genome.ucsc.edu//getData/track?genome=hg38&track=cloneEndRP11&chrom=chr1&start=1&end=248956420 API and load Data for BED file type. | Develop code to connect to this https://api.genome.ucsc.edu//getData/track?genome=hg38&track=ReMapDensity&chrom=chr1&start=1&end=248956 API and load Data for BED file type. |
| Description | Develop code to connect to this https://api.genome.ucsc.edu//getData/track?genome=hg38&track=ReMapDensity&chrom=chr1&start=1&end=248956 API and load Data for BED file type. | Develop code to connect to this https://api.genome.ucsc.edu//getData/track?genome=hg38&track=ReMapDensity&chrom=chr1&start=1&end=248956 API and load Data for the Wiggle file type. |
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| Issue Type | Sub-task [ 5 ] | Task [ 3 ] |
| Epic Link |
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| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 7, Fall 8, Spring 1, Spring 2, Spring 3 [ 183, 184, 185, 186, 187 ] | Fall 7, Fall 8, Spring 1, Spring 2, Spring 3, Spring 4 [ 183, 184, 185, 186, 187, 188 ] |
| Rank | Ranked higher |
| Attachment | Screenshot 2024-02-20 at 1.27.33 PM.png [ 18226 ] |
| 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 ] |
Testing on Mac
Testing wig file format with this API call - I am able to select the phastCons77way track, go to chr23:6,048,722-6,118,695 in the galGal6 genome, and click Load Data. Data appear correctly, no issues in log. However, when I zoom in the data disappear. When using the Selection Info track, I see a y coord of "no point" or "0". If I go to the Graph tab and select Save Graph, the file contains the correct data, and when I load the new graph in IGB, the graph works correctly. So the data are present in IGB, but they are not displaying correctly for some reason.
See dataDisappearing_WIG.png and example.wig files for comparison.
Testing bigwig with this API call - I am able to add and load the data successfully, everything looks good.
| Attachment | example.wig [ 18229 ] |
| Attachment | dataDisappearing_WIG.png [ 18230 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Screenshot 2024-02-22 at 2.11.26 PM.png [ 18242 ] |
| Attachment | Screenshot 2024-02-22 at 2.21.22 PM.png [ 18243 ] |
| Attachment | Screenshot 2024-02-22 at 2.44.40 PM.png [ 18244 ] |
Fixed the issue graph disappearing issue for the wig format file by adding sort on X values, the same way it's been done while manually loading a wig file. Tested the code, working as expected. Attached the screenshots below. Code is available at the branch https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
phastCons77way appearing correctly in IGB.
Closing ticket.
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| 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 ] |
| Fix Version/s | 10.1.0 [ 11000 ] |
Implemented the code to load the wiggle format files (both bigWig and wig formats), and used existing GraphIntervalSym to load the syms. Testing is also done, working as expected. Didn't add the wigMaf file format as it's a bit different from the wiggle file formats: https://api.genome.ucsc.edu/getData/track?genome=hg38&track=multiz100way&chrom=chr1&start=8372&end=33172, Nowlan Freese Could you please check this format once and let me know whether it's okay to treat it as a wig format.
Code is available at branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501.
To test: