Bsweger/get clades list #18
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
There are a few changes (for example, sorting by date and clade before slicing on the "n" clades that create the final list). This changeset also adds test cases for various permutations of threshold, threshold_weeks, and the maximum number of clades allowed in the list being returned.
bsweger
commented
Sep 9, 2024
bsweger
commented
Sep 9, 2024
bsweger
commented
Sep 9, 2024
| # FIXME: provide ability to instantiate Config for the get_clade_list function and get the data_path from there | ||
| def main( | ||
| genome_metadata_path: AnyPath = Config.nextstrain_latest_genome_metadata, | ||
| data_dir: AnyPath = AnyPath(".").home() / "covid_variant", |
There was a problem hiding this comment.
As with @rogersbw original code, we're saving the Nextstrain metadata to disk so we can work with it locally. I'm assuming that this is an internal concern (for example, we don't need to surface the download to whatever process runs get_clade_list and could change this implementation detail if needed).
Please let me know if that assumption is incorrect!
bsweger
commented
Sep 9, 2024
| def main( | ||
| genome_metadata_path: AnyPath = Config.nextstrain_latest_genome_metadata, | ||
| data_dir: AnyPath = AnyPath(".").home() / "covid_variant", | ||
| threshold: float = 0.01, |
There was a problem hiding this comment.
These defaults are from the original clades_to_model code: https://github.com/rogersbw/clade_data_utils/blob/main/utility/data_utility.py#L79
bsweger
commented
Sep 9, 2024
bsweger
commented
Sep 9, 2024
bsweger
commented
Sep 9, 2024
|
This all looks good to me. Merging! |
rogersbw
approved these changes
Sep 9, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Resolves #13
Also see comments here about why I deviated from the original plan of putting this function in the hub itself.
This PR continues the work to port @rogersbw's "clades to model" process into
virus-clade-utils:sequence.pyget_clade_list.py, which returns a list of clades to model, based on 3 criteria:Note that
get_clade_list.pyreturns "clades to model" as a Python list, with the assumption that it will be serialized and written to disk by the calling process (e.g., the variant nowcast hub). We'll need to think about that more, since that hub's "make round config" code is written in R.