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: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 9, Spring 10
Description
Situation: When a user selects a genome in IGB the default gene annotation (usually RefGene) for that genome is loaded automatically (Load Mode = Genome). With the addition of new genomes from UCSC REST endpoint that are not part of IGB Quickload, it would be nice for users if we would load a gene annotation automatically.
Task: Investigate if we can check to see if a genome version is not being provided by IGB Quickload. If it is not, but the UCSC REST genome annotation is available (RefGene, for example), load the UCSC REST annotation.
Attachments
Activity
Added code to load the UCSC Rest refGene track (only one chromosome) when IGB Quickload isn't available for that gene. Updated code is available at the branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3633. Tested working as expected.
To Test:
- Build the jar file for the branch in your local or download the installer.
- Start the application and select any species that doesn't have data in IGB Quickload.
- You should see data is being loaded automatically for the first chromosome if the gene has the refGene track and has data for that first chromosome.
Below are a few scenarios that were tested, and outputs were discussed with Nowlan Freese as well.
Scenario-1:
IGB Quickload is not present and the gene has refGene track in the UCSC Rest dataset and it has data as well for the first chromosome
Scenario-2:
IGB Quickload is not present and the gene has refGene track in the UCSC Rest dataset and it doesn't have data for the first chromosome. Empty track will be loaded
(Reason for this is list of chromosomes are being loaded in the start so we use this UCSC API to get the chromosomes https://api.genome.ucsc.edu/list/chromosomes?genome=allMis1 which has all the chromosomes across all the tracks, where as the specific track may contain a subset of them, for example you can find only 54 chromosomes in this track https://api.genome.ucsc.edu/list/chromosomes?genome=allMis1;track=refGene out of the 14645 chromosomes listed in the main API)
Scenario-3:
IGB Quickload is not present and the gene doesn't have refGene track in the UCSC Rest dataset: Track doesn't load at all
Tested Sravani's branch on Mac. Data are being loaded for the default chromosome from refGene (if available) in genomes that are only available from UCSC REST.
If UCSC is unavailable prior to the user starting IGB, the UCSC REST data provider is marked in red and the genomes are not available. If UCSC goes down after a user has selected a genome only available through UCSC REST, then data do not load and a 400 error can be found in the logs. This should be the intended behavior.
Ready for pull request.
Raised the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1013. Please review and let me know if there are any issues.
PR is merged. Installers are built and deployed to bioviz.org "early access" section.
Tested on main branch installer on Mac.
Selecting a genome provided only by UCSC REST, such as newer versions of Gallus gallus or Xenopus tropicalis, results in the first/default chromosome loading data from UCSC REST refGene. Loading a genome where IGB Quickload data is available (human hg38) results in the default IGB Quickload annotation loading and no data by default loading from UCSC REST.
Closing ticket.
I have noticed that genomes with many chromosomes/fragments (hundreds to thousands) tend to load very slowly when Load Mode = Genome. We may just want to load the gene annotation (RefGene) for whichever chromosome is displayed to the user. That way the IGB window does not appear blank, but the user doesn't have to wait several minutes for the entire genomes gene annotation to load.