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  1. IGB
  2. IGBF-3657

Implement logic to load data for narrowPeak file type

    Details

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

      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

          Hide
          jsirigin Jaya Sravani Sirigineedi added a comment -

          Use logic in the parseLineToDataModel method in NarrowPeak Symloader class to create parsing logic for narrowPeak file type in the UCSC Rest API module.

          Show
          jsirigin Jaya Sravani Sirigineedi added a comment - Use logic in the parseLineToDataModel method in NarrowPeak Symloader class to create parsing logic for narrowPeak file type in the UCSC Rest API module.
          Hide
          jsirigin Jaya Sravani Sirigineedi added a comment - - edited

          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:

          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-3657 and start the application.
          2. Select a particular genome. (note: hg38 has data for this track)
          3. Select any narrowPeak track (dataset) type.
          4. Click on the load data button either from the top right corner or in the data management table.
          5. Check whether the data is loaded correctly and the peak is visible.

          Show
          jsirigin Jaya Sravani Sirigineedi added a comment - - edited 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.
          Hide
          nfreese Nowlan Freese added a comment -

          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.

          Show
          nfreese Nowlan Freese added a comment - 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.
          Hide
          jsirigin Jaya Sravani Sirigineedi added a comment -

          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.

          Show
          jsirigin Jaya Sravani Sirigineedi added a comment - 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.
          Hide
          ann.loraine Ann Loraine added a comment -

          Merged.

          Show
          ann.loraine Ann Loraine added a comment - Merged.
          Hide
          ann.loraine Ann Loraine added a comment - - edited

          New PR is merged. New "early access" installers are built and deployed to BioViz.org.

          Show
          ann.loraine Ann Loraine added a comment - - edited New PR is merged. New "early access" installers are built and deployed to BioViz.org.
          Hide
          nfreese Nowlan Freese added a comment -

          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.

          Show
          nfreese Nowlan Freese added a comment - 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.

            People

            • Assignee:
              jsirigin Jaya Sravani Sirigineedi
              Reporter:
              jsirigin Jaya Sravani Sirigineedi
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              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: