Skip to content
New issue

Have a question about this project? # for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “#”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? # to your account

Error using custom reference genome #22

Open
alimanfoo opened this issue Nov 16, 2021 · 0 comments
Open

Error using custom reference genome #22

alimanfoo opened this issue Nov 16, 2021 · 0 comments

Comments

@alimanfoo
Copy link

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
# for free to join this conversation on GitHub. Already have an account? # to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant