pg-sui 1.0.2.1__py3-none-any.whl → 1.6.8__py3-none-any.whl

test/test_tkc.py

@@ -1,214 +0,0 @@
-import sys
-import os
-import copy
-import unittest
-import pprint
-from pgsui.impute.estimators import (
-    ImputeKNN,
-    ImputeRandomForest,
-    ImputeXGBoost,
-    ImputeVAE,
-    ImputeStandardAutoEncoder,
-    ImputeUBP,
-    ImputeNLPCA,
-)
-from pgsui.impute.simple_imputers import (
-    ImputePhylo,
-    ImputeMF,
-    ImputeAlleleFreq,
-    ImputeRefAllele,
-)
-
-from snpio import GenotypeData
-from pgsui.data_processing.transformers import SimGenotypeDataTransformer
-import numpy as np
-
-
-class HiddenPrints:
-    def __enter__(self):
-        self._original_stdout = sys.stdout
-        sys.stdout = open(os.devnull, "w")
-
-    def __exit__(self, exc_type, exc_val, exc_tb):
-        sys.stdout.close()
-        sys.stdout = self._original_stdout
-
-
-class TestMyClasses(unittest.TestCase):
-    def setUp(self):
-        with HiddenPrints():
-            self.genotype_data = GenotypeData(
-                filename="pgsui/example_data/phylip_files/test_n100.phy",
-                popmapfile="pgsui/example_data/popmaps/test.popmap",
-                guidetree="pgsui/example_data/trees/test.tre",
-                qmatrix="pgsui/example_data/trees/test.qmat",
-                siterates="pgsui/example_data/trees/test_siterates_n100.txt",
-                prefix="test_imputer",
-                force_popmap=True,
-                plot_format="png",
-            )
-
-            # Create a SimGenotypeDataTransformer instance and use it
-            # to simulate missing data
-            self.transformer = SimGenotypeDataTransformer(
-                genotype_data=self.genotype_data,
-                prop_missing=0.2,
-                strategy="random_weighted",
-            )
-            self.transformer.fit(self.genotype_data.genotypes_012(fmt="numpy"))
-            self.simulated_data = self.genotype_data.copy()
-
-            self.simulated_data.genotypes_012 = self.transformer.transform(
-                self.genotype_data.genotypes_012(fmt="numpy")
-            )
-
-    def _test_class(self, class_instance, do_gridsearch=False):
-        print(f"\nMETHOD: {class_instance.__name__}\n")
-
-        if do_gridsearch:
-            # Do a simple test.
-            if class_instance in [ImputeRandomForest, ImputeXGBoost]:
-                param_grid = {"n_estimators": [50, 100]}  # Do a simple test
-            elif class_instance in [
-                ImputeVAE,
-                ImputeStandardAutoEncoder,
-                ImputeNLPCA,
-                ImputeUBP,
-            ]:
-                param_grid = {"dropout_rate": [0.1, 0.2]}
-            elif class_instance == ImputeKNN:
-                param_grid = {"n_neighbors": [5, 8]}
-        else:
-            param_grid = None
-
-        kwargs = {
-            'sim_strategy': "random_weighted"
-        }
-
-        instance = class_instance(
-            self.simulated_data, 
-            gridparams=param_grid, 
-            **kwargs)
-
-        # Write the masks
-        self.transformer.write_mask(filename_prefix="mask_test")
-
-        imputed_data = instance.imputed.genotypes_012(fmt="numpy")
-
-        # Test that the imputed values are close to the original values
-        accuracy = self.transformer.accuracy(
-            self.genotype_data.genotypes_012(fmt="numpy"), imputed_data
-        )
-
-        (
-            auc_roc_scores,
-            precision_scores,
-            recall_scores,
-            avg_precision_scores,
-        ) = self.transformer.auc_roc_pr_ap(
-            self.genotype_data.genotypes_012(fmt="numpy"), imputed_data
-        )
-
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"OVERALL ACCURACY: {accuracy}"
-        )
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"AUC-ROC PER CLASS: {dict(zip(range(3), auc_roc_scores))}"
-        )
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"PRECISION PER CLASS: {dict(zip(range(3), precision_scores))}"
-        )
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"RECALL PER CLASS: {dict(zip(range(3), recall_scores))}"
-        )
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"AVERAGE PRECISION PER CLASS: {dict(zip(range(3), avg_precision_scores))}"
-        )
-
-        # Read masks from file
-        self.transformer.read_mask(filename_prefix="mask_test")
-
-        # Recalculate accuracy after reading in the mask
-        accuracy_after_read = self.transformer.accuracy(
-            self.genotype_data.genotypes_012(fmt="numpy"), imputed_data
-        )
-
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"OVERALL ACCURACY AFTER READ: {accuracy_after_read}"
-        )
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"AUC-ROC PER CLASS AFTER READ: {dict(zip(range(3), auc_roc_scores))}"
-        )
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"PRECISION PER CLASS AFTER READ: {dict(zip(range(3), precision_scores))}"
-        )
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"RECALL PER CLASS AFTER READ: {dict(zip(range(3), recall_scores))}"
-        )
-        pprint.PrettyPrinter(indent=4, sort_dicts=True).pprint(
-            f"AVERAGE PRECISION PER CLASS AFTER READ: {dict(zip(range(3), avg_precision_scores))}"
-        )
-
-
-        print("\n")
-
-    # def test_ImputeKNN(self):
-    #     self._test_class(ImputeKNN)
-
-    # def test_ImputeRandomForest(self):
-    #     self._test_class(ImputeRandomForest)
-
-    # def test_ImputeXGBoost(self):
-    #     self._test_class(ImputeXGBoost)
-
-    def test_ImputeVAE(self):
-        self._test_class(ImputeVAE)
-
-    # def test_ImputeStandardAutoEncoder(self):
-    #     self._test_class(ImputeStandardAutoEncoder)
-
-    # def test_ImputeUBP(self):
-    #     self._test_class(ImputeUBP)
-
-    # def test_ImputeNLPCA(self):
-    #     self._test_class(ImputeNLPCA)
-
-    # def test_ImputeKNN_grid(self):
-    #     self._test_class(ImputeKNN, do_gridsearch=True)
-
-    # def test_ImputeRandomForest_grid(self):
-    #     self._test_class(ImputeRandomForest, do_gridsearch=True)
-
-    # def test_ImputeXGBoost_grid(self):
-    #     self._test_class(ImputeXGBoost, do_gridsearch=True)
-
-    # def test_ImputeVAE_grid(self):
-    #     self._test_class(ImputeVAE, do_gridsearch=True)
-
-    # def test_ImputeStandardAutoEncoder_grid(self):
-    #     self._test_class(ImputeStandardAutoEncoder, do_gridsearch=True)
-
-    # def test_ImputeUBP_grid(self):
-    #     self._test_class(ImputeUBP, do_gridsearch=True)
-
-    # def test_ImputeNLPCA_grid(self):
-    #     self._test_class(ImputeNLPCA, do_gridsearch=True)
-
-    # def test_ImputePhylo(self):
-    #     self._test_class(ImputePhylo)
-
-    # def test_ImputeAlleleFreq(self):
-    #     self._test_class(ImputeAlleleFreq)
-
-    # def test_ImputeRefAllele(self):
-    #     self._test_class(ImputeRefAllele)
-
-    # def test_ImputeMF(self):
-    #     self._test_class(ImputeMF)
-
-    # def test_ImputeRefAllele(self):
-    #     self._test_class(ImputeRefAllele)
-
-
-if __name__ == "__main__":
-    unittest.main()