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.

Sign up for GitHub

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

Jump to bottom

read_plink from cloud storage #1150

Open
hammer opened this issue Dec 2, 2023 · 1 comment
Open

read_plink from cloud storage #1150

hammer opened this issue Dec 2, 2023 · 1 comment
Labels
IO Issues related to reading and writing common third-party file formats

Comments

@hammer
Copy link
Contributor

hammer commented Dec 2, 2023

We are able to read VCF files from cloud storage thanks to support in htslib for some functions and fsspec for others.

For PLINK BED files, I don't believe we have this option in our upstream library https://github.com/fastlmm/bed-reader. For BIM and FAM files, we use Dask's read_csv function, which does use fsspec, though we don't currently pass storage_options through.

It may make sense to try to support reading PLINK files from cloud storage some day...
@hammer hammer added the IO Issues related to reading and writing common third-party file formats label Dec 2, 2023
@hammer
Copy link
Contributor Author

hammer commented Jan 11, 2024

Issue opened upstream at fastlmm/bed-reader#22

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
IO Issues related to reading and writing common third-party file formats
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@hammer