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
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.
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().