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:Fall 6, Fall 7
Description
Situation: Investigate the UCSC REST API to understand what data are available and how they are organized
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Sprint | Fall 6 [ 182 ] | Fall 6, Fall 7 [ 182, 183 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
DasSymloader is used to get segment region specific feature information, to implement this we have to use the https://api.genome.ucsc.edu/getData/track?genome=hg16;track=refGene;chrom=chr1;start=1;end=100000 api for the rest module.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| 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 ] |
To get the UCSC available genomes use this https://api.genome.ucsc.edu/list/ucscGenomes API and create a similar method like initialize() available in the DasDataProvider in the new UCSC API module. To get the available datasets for a genome use https://api.genome.ucsc.edu/list/tracks?genome=hg38 this api and implement a method similar to getAvailableDataSets(). Also, implement methods that connect to https://api.genome.ucsc.edu/list/chromosomes?genome=hg38 to get the chromosomes for a selected genome, similar to getAssemblyInfo() in DasDataProvider and https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678 api to get the sequence for a particular region, similar to method getSequence().