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Description
Bug report
Trying to instantiate a browser with a custom reference genome doesn't seem to work.
import ipyigv as igv
from ipyigv.options import ReferenceGenome, Track
print(igv.__version__)
genomeDict = {
'name': "AgamP4",
'fastaURL': "https://storage.googleapis.com/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa",
'indexURL': "https://storage.googleapis.com/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai",
}
genome = ReferenceGenome(**genomeDict)
browser = igv.IgvBrowser(genome=genome)
browser
Actual outcome
Browser appears, but no chromosomes appear in the dropdown, and an error appears in the browser developer console.
In the browser developer console I get:
Uncaught (in promise) TypeError: Cannot read properties of undefined (reading 'rangeLocus')
at e.value (138.93ff5122a91b7d500341.js:2)
at e.<anonymous> (138.93ff5122a91b7d500341.js:2)
at h (138.93ff5122a91b7d500341.js:2)
at Generator._invoke (138.93ff5122a91b7d500341.js:2)
at Generator.next (138.93ff5122a91b7d500341.js:2)
at vr (138.93ff5122a91b7d500341.js:2)
at o (138.93ff5122a91b7d500341.js:2)
Expected outcome
IGV browser appears and chromosomes are visible.
Version Info
Run on ipyigv binder in jupyter lab.
- ipyigv version: 0.1.9
- Python version: 3.7.10
- Jupyter lab version: 3.1.11
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