Skip to content
New issue

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

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

Already on GitHub? Sign in to your account

including repeats in annotation data for querying #65

Open
2 tasks
GavinHuttley opened this issue Jan 30, 2024 · 1 comment
Open
2 tasks

including repeats in annotation data for querying #65

GavinHuttley opened this issue Jan 30, 2024 · 1 comment
Labels
enhancement New feature or request

Comments

@GavinHuttley
Copy link

GavinHuttley commented Jan 30, 2024

Minimal data for repeat information is:

  • genomic coordinates (coordinate name, start, end, strand)
  • repeat classification information, including repeat type, repeat class, score (?)

What is the minimum data needed to download that will provide this? (That is, what are the minimum files required.)

Conceptually separate the download from the install step. The former grabs data in a sufficiently complete form that the install step does not require internet access.

We then need to transform this to be compatible with the querying approach for gene features, perhaps a single table.

@GavinHuttley GavinHuttley added the enhancement New feature or request label Jan 30, 2024
@EbiArnie
Copy link

This should cover the repeats:
https://github.com/EbiArnie/EnsemblLite/blob/exp/duckdb/experiments/dd_fetch_repeats.py

I don't feel this is ready to be a PR just yet.

The next step would be to integrate this in a smart way. We just talked about that - this would probably replace or augment the current data fetching methods available in EnsemblLite.

@GavinHuttley GavinHuttley added this to the robust-usability milestone May 16, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants