Add Deep DNAshape backend option to ShapeME#29
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vivianra wants to merge 3 commits intofreddolino-lab:mainfrom
Open
Add Deep DNAshape backend option to ShapeME#29vivianra wants to merge 3 commits intofreddolino-lab:mainfrom
vivianra wants to merge 3 commits intofreddolino-lab:mainfrom
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…Ashape dependencies, updated create_synthetic_data.py to allow for class imbalance options
…the option for DNAshape features inference
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This pull request adds Deep DNAshape as an optional backend for computing DNA shape features in ShapeME. It also extends the create_synthetic_data.py utility to allow generation of synthetic datasets with user-defined class imbalance.
Changes include:
--shape_toolargument toShapeME.py, allowing users to select between DNAshapeR and DeepDNAshape. DNAshapeR remains the default backend.calc_deepdnashape.pyutility script, which invokes DeepDNAshape to compute DNA shape features.deepdnashape_env.yamlfile to provide the dependencies required for running DeepDNAshape.shapeme.defto include the DeepDNAshape environment.--cat_weightsargument tocreate_synthetic_data.py, allowing users to specify class imbalance when generating synthetic datasets.These features were added in response to reviewer comments requesting support for more recent DNA shape prediction methods and class imbalance synthetic datasets.