[IGBF-3557] Implement an API to get the dna sequence for the selected genome region span - JIRA UNCC

Details

Type: Sub-task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 10.1.0
Labels:
None

Story Points:
2
Sprint:
Fall 7, Fall 8, Spring 1, Spring 2, Spring 3

Description

Develop code to integrate this API (https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=1;end=16569) to get the dna sequence

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26/Jan/24 4:21 PM

Activity

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Jaya Sravani Sirigineedi created issue - 23/Jan/24 10:30 AM

Jaya Sravani Sirigineedi made changes - 24/Jan/24 7:42 PM

Field	Original Value	New Value
Status	To-Do [ 10305 ]	In Progress [ 3 ]

Jaya Sravani Sirigineedi made changes - 26/Jan/24 4:21 PM

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Screenshot 2024-01-26 at 4.09.10 PM.png [ 18185 ]

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Jaya Sravani Sirigineedi added a comment - 26/Jan/24 4:21 PM

Developed code to integrate the API and get dna sequence for the selected genome and the selected chromosome of a particular span region. Tested it and working as expected. Code is available at the 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.
Click on the load sequence button from the top right corner and zoom the view horizontally to check whether the sequence appears near the coordinate tier.

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Jaya Sravani Sirigineedi added a comment - 26/Jan/24 4:21 PM Developed code to integrate the API and get dna sequence for the selected genome and the selected chromosome of a particular span region. Tested it and working as expected. Code is available at the 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. Click on the load sequence button from the top right corner and zoom the view horizontally to check whether the sequence appears near the coordinate tier.

Jaya Sravani Sirigineedi made changes - 26/Jan/24 4:21 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Jaya Sravani Sirigineedi made changes - 26/Jan/24 4:21 PM

Assignee

Jaya Sravani Sirigineedi [ jsirigin ]

Nowlan Freese made changes - 30/Jan/24 2:11 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

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Nowlan Freese added a comment - 30/Jan/24 2:22 PM

Tested on Mac.

I disabled all Data Sources except for UCSC REST. I was able to load sequence for human, alligator, and chicken genomes.

Example Log:

Completed loading sequence for chr1 : 134,527,209 - 134,527,252 from UCSC REST https://api.genome.ucsc.edu/

Closing ticket.

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Nowlan Freese added a comment - 30/Jan/24 2:22 PM Tested on Mac. I disabled all Data Sources except for UCSC REST. I was able to load sequence for human, alligator, and chicken genomes. Example Log: Completed loading sequence for chr1 : 134,527,209 - 134,527,252 from UCSC REST https: //api.genome.ucsc.edu/ Closing ticket.