ENH: Move pairs_to_features and generate_kmer_vecs to transformer interface (#174)#628
Open
DashratRajpurohit wants to merge 1 commit intogc-os-ai:mainfrom
Open
Conversation
…erface (gc-os-ai#174) - Added KMerFeatures and AptaNetFeatures to pyaptamer.trafos.features that inherit from BaseTransform. - Deprecated pairs_to_features and generate_kmer_vecs in pyaptamer.utils._aptanet_utils. - Updated AptaNetPipeline to use AptaNetFeatures instead of FunctionTransformer.
This file contains hidden or 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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Closes #174.
Overview
This PR addresses the "Redesigning the Public and Internal API" roadmap project by moving
generate_kmer_vecsandpairs_to_featuresto the properBaseTransforminterface, standardizing their behavior with the rest of thetrafosmodule (following theGreedyEncodertemplate).Changes Made
KMerFeaturesinpyaptamer/trafos/features/_kmer.py.AptaNetFeaturesinpyaptamer/trafos/features/_aptanet.py.BaseTransformand return Pandas DataFrames.AptaNetPipelineto useAptaNetFeaturesinstead ofFunctionTransformer.list of tuplesinputs from users still work transparently.DeprecationWarnings topairs_to_featuresandgenerate_kmer_vecsin_aptanet_utils.py, directing users to the newtrafos.featuresclasses.This sets up a much cleaner architectural foundation for future
trafosfeature extractors.