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, Spring 5
Description
Develop code to connect to this https://api.genome.ucsc.edu/getData/track?genome=hg19;track=xenoMrna;chrom=chrM API and load Data for PSL file type.
Attachments
Activity
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Screenshot 2024-02-06 at 11.47.53 AM.png [ 18206 ] |
| Attachment | Screenshot 2024-02-06 at 11.57.22 AM.png [ 18207 ] |
Fixed the issue and tested, working as expected. Code is available at branch https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501.
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-3501 and start the application.
- Select a particular genome, preferably one that doesn't have data in IGB quick load.
- Select a PSL track (dataset) type.
- Click on the load data button either from the top right corner or in the data management table.
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Description | Develop code to connect to this https://api.genome.ucsc.edu/getData/track?genome=hg19;track=refGene;chrom=chrM API and load Data only for genePred file type for now. | Develop code to connect to this https://api.genome.ucsc.edu/getData/track?genome=hg19;track=refGene;chrom=chrM API and load Data for PSL file type. |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Description | Develop code to connect to this https://api.genome.ucsc.edu/getData/track?genome=hg19;track=refGene;chrom=chrM API and load Data for PSL file type. | Develop code to connect to this https://api.genome.ucsc.edu/getData/track?genome=hg19;track=xenoMrna;chrom=chrM API and load Data for PSL file type. |
Tested on mouse genome (mm39) on Mac using Sravani's installer.
In IGB, navigate to chr1:60,380,220-60,429,457
Load data from UCSC REST > mRNA
Load data from IGB Quickload > mRNA
The two files matched very closely, which is expected, as the IGB Quickload mRNA file was created from the UCSC Table Browser as a psl file (see IGBF-3330).
The API call for the same data is: https://api.genome.ucsc.edu/getData/track?genome=mm39;track=all_mrna;chrom=chr1;start=60380220;end=60429457
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 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
Reopening the ticket, as while testing it again I found that a few strands are not displaying currently mostly in the negative area. Found one problem in the code, investigating how to solve it.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Screenshot 2024-02-27 at 3.48.26 PM.png [ 18259 ] |
Fixed the issue by changing the logic of the calculation of the same orientation, blockSizes, qmins, and tmins by using the already existing function in the AbstractPSLParser class. Attached screenshots below to see he difference. also, code is available at https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501.
Before:
After:
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Parent |
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| Issue Type | Sub-task [ 5 ] | Task [ 3 ] |
| Epic Link |
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| 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 ] |
| Sprint | Fall 7, Fall 8, Spring 1, Spring 2, Spring 3, Spring 4 [ 183, 184, 185, 186, 187, 188 ] | Fall 7, Fall 8, Spring 1, Spring 2, Spring 3, Spring 4, Spring 5 [ 183, 184, 185, 186, 187, 188, 189 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
I compared the xenoMrna as loaded from UCSC Rest to the xenoMrna file I pulled from the UCSC table browser. The allMis_JH738473_xenoMrna.psl file should effectively be the same data as what is provided by UCSC Rest, and as far as I can tell they appear the same when loaded in IGB.
See IGBF-3330 for instructions on creating a psl file from the UCSC Table Browser.
Closing ticket.
| 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 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Attachment | allMis_JH738473_xenoMrna.psl [ 18288 ] |
| Fix Version/s | 10.1.0 [ 11000 ] |
Code development is done for the PSL file type, while testing found out that the track name is changing to "Pairwise Alignment" debugging this issue now, but apart from that the data loading is being done correctly.
