pg-sui 1.6.14.dev9__py3-none-any.whl → 1.7.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pg_sui-1.7.0.dist-info/METADATA +288 -0
- {pg_sui-1.6.14.dev9.dist-info → pg_sui-1.7.0.dist-info}/RECORD +29 -33
- pgsui/__init__.py +0 -8
- pgsui/_version.py +2 -2
- pgsui/cli.py +591 -126
- pgsui/data_processing/config.py +1 -2
- pgsui/data_processing/containers.py +218 -533
- pgsui/data_processing/transformers.py +44 -20
- pgsui/impute/deterministic/imputers/mode.py +475 -182
- pgsui/impute/deterministic/imputers/ref_allele.py +454 -147
- pgsui/impute/supervised/imputers/hist_gradient_boosting.py +4 -3
- pgsui/impute/supervised/imputers/random_forest.py +3 -2
- pgsui/impute/unsupervised/base.py +1268 -530
- pgsui/impute/unsupervised/callbacks.py +28 -33
- pgsui/impute/unsupervised/imputers/autoencoder.py +869 -764
- pgsui/impute/unsupervised/imputers/vae.py +928 -696
- pgsui/impute/unsupervised/loss_functions.py +156 -202
- pgsui/impute/unsupervised/models/autoencoder_model.py +7 -49
- pgsui/impute/unsupervised/models/vae_model.py +40 -221
- pgsui/impute/unsupervised/nn_scorers.py +53 -13
- pgsui/utils/classification_viz.py +240 -97
- pgsui/utils/misc.py +201 -3
- pgsui/utils/plotting.py +73 -58
- pgsui/utils/pretty_metrics.py +2 -6
- pgsui/utils/scorers.py +39 -0
- pg_sui-1.6.14.dev9.dist-info/METADATA +0 -344
- pgsui/impute/unsupervised/imputers/nlpca.py +0 -1554
- pgsui/impute/unsupervised/imputers/ubp.py +0 -1575
- pgsui/impute/unsupervised/models/nlpca_model.py +0 -206
- pgsui/impute/unsupervised/models/ubp_model.py +0 -200
- {pg_sui-1.6.14.dev9.dist-info → pg_sui-1.7.0.dist-info}/WHEEL +0 -0
- {pg_sui-1.6.14.dev9.dist-info → pg_sui-1.7.0.dist-info}/entry_points.txt +0 -0
- {pg_sui-1.6.14.dev9.dist-info → pg_sui-1.7.0.dist-info}/licenses/LICENSE +0 -0
- {pg_sui-1.6.14.dev9.dist-info → pg_sui-1.7.0.dist-info}/top_level.txt +0 -0
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@@ -209,8 +209,9 @@ class ImputeHistGradientBoosting(BaseImputer):
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X_int = self.pgenc.genotypes_012
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self.X012_ = X_int.astype(float)
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self.X012_[self.X012_ < 0] = np.nan # Ensure missing are NaN
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self.
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self.
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self.ploidy = self.cfg.io.ploidy
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self.is_haploid = self.ploidy == 1
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self.num_classes_ = 2 if self.is_haploid else 3
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self.n_samples_, self.n_features_ = X_int.shape
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# Split
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@@ -296,7 +297,7 @@ class ImputeHistGradientBoosting(BaseImputer):
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This method applies the trained imputer to the entire dataset, filling in missing genotype values. It ensures that any remaining missing values after imputation are set to -9, and decodes the imputed 0/1/2 genotypes back to their original format.
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Returns:
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np.ndarray: (n_samples, n_loci)
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np.ndarray: (n_samples, n_loci) IUPAC strings (single-character codes).
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Raises:
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NotFittedError: If fit() has not been called prior to transform().
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@@ -185,7 +185,8 @@ class ImputeRandomForest(BaseImputer):
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X_int = self.pgenc.genotypes_012
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self.X012_ = X_int.astype(float)
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self.X012_[self.X012_ < 0] = np.nan # Ensure missing are NaN
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self.
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self.ploidy = self.cfg.io.ploidy
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self.is_haploid = self.ploidy == 1
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self.num_classes_ = 2 if self.is_haploid_ else 3
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self.n_samples_, self.n_features_ = X_int.shape
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@@ -273,7 +274,7 @@ class ImputeRandomForest(BaseImputer):
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This method applies the trained imputer to the entire dataset, filling in missing genotype values. It ensures that any remaining missing values after imputation are set to -9, and decodes the imputed 0/1/2 genotypes back to their original format.
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Returns:
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np.ndarray: (n_samples, n_loci)
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np.ndarray: (n_samples, n_loci) IUPAC strings (single-character codes).
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"""
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if not self.is_fit_:
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msg = "Imputer has not been fit; call fit() before transform()."
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