Functional refactor #81
Open
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
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Outdated suggestions cannot be applied.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.
Functional Refactor of crested.tl.Crested(...) class
In this large refactor I'm moving everything from the Crested class that does not use both a model and the AnnDatamodule out to a new _tools.py module where everything will be functional.
All the old functions remain in the Crested class for backward compatibility (for now) but will now raise a deprecation warning.
I'm giving up a bit of clarity for ease of use by combining functions that do the same on different inputs into one single function.
Equivalent new functions
tl.Crested.get_embeddings(...)--->tl.extract_layer_embeddings(...)tl.Crested.predict(...)--->tl.predict(...)tl.Crested.predict_regions(...)--->tl.predict(...)tl.Crested.predict_sequence(...)--->tl.predict(...)tl.Crested.score_gene_locus(...)--->tl.score_gene_locus(...)tl.Crested.calculate_contribution_scores(...)--->tl.contribution_scores(...)tl.Crested.calculate_contribution_scores_regions(...)--->tl.contribution_scores(...)tl.Crested.calculate_contribution_scores_sequence(...)--->tl.contribution_scores(...)tl.Crested.calculate_contribution_scores_enhancer_design(...)--->tl.contribution_scores(...)tl.Crested.tfmodisco_calculate_and_save_contribution_scores_sequences--->tl.contribution_scores_specific(...)tl.Crested.tfmodisco_calculate_and_save_contribution_scores--->tl.contribution_scores(...)tl.Crested.enhancer_design_motif_implementation--->