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  1. IGB
  2. IGBF-3503 Implement UCSC REST API logic in IGB
  3. IGBF-3557

Implement an API to get the dna sequence for the selected genome region span

        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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              jsirigin Jaya Sravani Sirigineedi added a comment -

              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:

              1. 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.
              2. Select a particular genome, preferably one that doesn't have data in IGB quick load.
              3. 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.
              Show
              jsirigin Jaya Sravani Sirigineedi added a comment - 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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              nfreese Nowlan Freese added a comment -

              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.

              Show
              nfreese Nowlan Freese added a comment - 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.

                People

                • Assignee:
                  jsirigin Jaya Sravani Sirigineedi
                  Reporter:
                  jsirigin Jaya Sravani Sirigineedi
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                  Dates

                  • Created:
                    Updated:
                    Resolved: