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2 class PredictInteraction:
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3
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4 def __init__(self, data = 'FeatureDataset'):
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5 import pickle
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6 from sklearn.preprocessing import LabelEncoder
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7 with open('files/' + data, 'rb') as f:
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8 self.dataset = pickle.load(f)
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9 self.dataset = self.dataset.dropna()
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10 le = LabelEncoder()
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11 le.fit(['Yes', 'No'])
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12 self.output = le.transform(self.dataset['Infects'].values)
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13 self.dataset = self.dataset.drop('Infects', 1)
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14 self.__standardize()
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15 self.__split_train_test()
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16
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17 def __standardize(self):
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18 from sklearn.preprocessing import StandardScaler
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19 self.scaler = StandardScaler()
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20 self.scaler.fit(self.dataset)
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21 self.data_z = self.scaler.transform(self.dataset)
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22
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23 def __cross_validation(self, method):
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24 from sklearn.model_selection import cross_val_score
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25 from sklearn.model_selection import StratifiedKFold
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26 # from sklearn.model_selection import ShuffleSplit
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27 # cv = ShuffleSplit(n_splits=4, test_size=0.3) # cross validation normal
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28 skf = StratifiedKFold(5, shuffle=True)
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29 scores = cross_val_score(method, self.data_z, self.output, cv=skf, scoring='f1_weighted')
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30 print(scores)
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31 return skf
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32
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33 def __split_train_test(self):
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34 from sklearn.model_selection import train_test_split
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35 self.data_z, self.X_val, self.output, self.y_val = train_test_split(self.data_z, self.output, test_size=0.2)
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36 self.X_train, self.X_test, self.y_train, self.y_test = train_test_split(self.data_z, self.output, test_size=0.3)
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37
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38 def run_knn(self, n=2):
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39 from sklearn.neighbors import KNeighborsClassifier
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40 from sklearn.metrics import confusion_matrix
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41 neigh = KNeighborsClassifier(n_neighbors=n, weights='distance', p=1, algorithm='brute')
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42 neigh.fit(self.X_train, self.y_train)
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43 # print(neigh.score(self.X_test, self.y_test))
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44 self.__score_metrics(neigh)
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45 # print(confusion_matrix(self.y_test, neigh.predict(self.X_test)))
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46 import time
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47 start_time = time.time()
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48 cv = self.__cross_validation(neigh)
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49 print("--- %s seconds ---" % (time.time() - start_time))
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50 # self.__plot_roc_cv(neigh, cv)
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51 # self.__auc_curve(neigh)
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52 self.__permutation_importance(self._hyperparameters_knn(neigh))
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53
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54 def _hyperparameters_knn(self, method):
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55 from sklearn.model_selection import GridSearchCV
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56 parameters = {'leaf_size': [5, 15, 30, 50], 'n_neighbors': [2, 3, 5, 7], 'weights': ['uniform', 'distance'], 'algorithm': ['auto', 'ball_tree', 'kd_tree', 'brute'], 'p': [1, 2]}
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57 clf = GridSearchCV(method, parameters)
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58 clf.fit(self.X_val, self.y_val)
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59 self.__score_metrics(clf)
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60 print(clf.best_params_)
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61 return clf
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62
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63 def run_random_forest(self):
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64 from sklearn.ensemble import RandomForestClassifier
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65 from sklearn.metrics import confusion_matrix
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66 clf = RandomForestClassifier(n_estimators=250, bootstrap=False, ccp_alpha=0.0, max_features='sqrt')
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67 clf = clf.fit(self.X_train, self.y_train)
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68 # print(clf.score(self.X_test, self.y_test))
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69 self.__score_metrics(clf)
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70 # print(confusion_matrix(self.y_test, clf.predict(self.X_test)))
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71 # self.recursive_feature_elimination(clf)
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72 import time
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73 start_time = time.time()
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74 cv = self.__cross_validation(clf)
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75 print("--- %s seconds ---" % (time.time() - start_time))
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76 # self.__plot_roc_cv(clf, cv)
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77 # self.__auc_curve(clf)
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78 # self.__permutation_importance(clf)
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79
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80 def _hyperparameters_rf(self, method):
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81 from sklearn.model_selection import GridSearchCV
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82 parameters = {'n_estimators': [50, 100, 150, 200, 250], 'criterion': ['gini', 'entropy'], 'min_samples_split': [2, 4, 6], 'min_samples_leaf': [2, 4, 6], 'bootstrap': [True, False], 'oob_score': [True, False]}
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83 clf = GridSearchCV(method, parameters)
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84 clf.fit(self.X_val, self.y_val)
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85 self.__score_metrics(clf)
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86 print(clf.best_params_)
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87 return clf
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88
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89 def run_svm(self, c=0.1):
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90 from sklearn.svm import SVC
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91 from sklearn.metrics import confusion_matrix
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92 svm = SVC(C=c)
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93 svm = svm.fit(self.X_train, self.y_train)
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94 # print(svm.score(self.X_test, self.y_test))
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95 self.__score_metrics(svm)
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96 # print(confusion_matrix(self.y_test, svm.predict(self.X_test)))
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97 import time
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98 start_time = time.time()
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99 cv = self.__cross_validation(svm)
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100 print("--- %s seconds ---" % (time.time() - start_time))
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101 # self.recursive_feature_elimination(svm)
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102 # self.__plot_roc_cv(svm, cv)
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103 # self.__auc_curve(svm)
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104 # self.__permutation_importance(svm)
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105
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106 def _hyperparameters_svm(self, method):
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107 from sklearn.model_selection import GridSearchCV
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108 parameters = {'C': [0.01, 0.1, 1, 10], 'kernel': ['linear','rbf','poly','sigmoid', 'precomputed'], 'degree': [2, 3, 4], 'gamma': ['scale', 'auto']}
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109 clf = GridSearchCV(method, parameters)
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110 clf.fit(self.X_val, self.y_val)
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111 self.__score_metrics(clf)
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112 print(clf.best_params_)
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113 return clf
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114
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115 def run_neural_networks(self, alpha=1):
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116 from sklearn.neural_network import MLPClassifier
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117 from sklearn.metrics import confusion_matrix
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118 clf = MLPClassifier(alpha=alpha)
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119 clf.fit(self.X_train, self.y_train)
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120 self.__score_metrics(clf)
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121 # print(confusion_matrix(self.y_test, clf.predict(self.X_test)))
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122 import time
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123 start_time = time.time()
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124 cv = self.__cross_validation(clf)
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125 print("--- %s seconds ---" % (time.time() - start_time))
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126 # self.__plot_roc_cv(clf, cv)
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127 # self.__auc_curve(clf)
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128 # self.__permutation_importance(clf)
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129
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130 def _hyperparameters_ann(self, method):
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131 from sklearn.model_selection import GridSearchCV
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132 parameters = {'hidden_layer_sizes': [50, 100, 200], 'activation': ['identity', 'logistic', 'tanh', 'relu'], 'solver': ['lbfgs', 'sgd', 'adam'], 'alpha': [0.0001, 0.05], 'learning_rate': ['constant', 'invscaling', 'adaptive']}
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133 clf = GridSearchCV(method, parameters)
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134 clf.fit(self.X_val, self.y_val)
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135 self.__score_metrics(clf)
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136 print(clf.best_params_)
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137 return clf
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138
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139 def run_logistic_reg(self, c=1):
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140 from sklearn.linear_model import LogisticRegression
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141 from sklearn.metrics import confusion_matrix
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142 clf = LogisticRegression(C=c)
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143 clf.fit(self.X_train, self.y_train)
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144 self.__score_metrics(clf)
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145 # print(confusion_matrix(self.y_test, clf.predict(self.X_test)))
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146 import time
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147 start_time = time.time()
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148 cv = self.__cross_validation(clf)
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149 print("--- %s seconds ---" % (time.time() - start_time))
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150 # self.__plot_roc_cv(clf, cv)
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151 # self.__auc_curve(clf)
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152 # self.__permutation_importance(clf)
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153
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154 def _hyperparameters_lr(self, method):
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155 from sklearn.model_selection import GridSearchCV
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156 parameters = {'penalty': ['l1', 'l2', 'elasticnet', 'none'], 'C': [0.01, 0.1, 1, 10], 'solver': ['lbfgs', 'liblinear', 'newton-cg', 'sag', 'saga']}
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157 clf = GridSearchCV(method, parameters)
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158 clf.fit(self.X_val, self.y_val)
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159 self.__score_metrics(clf)
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160 print(clf.best_params_)
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161 return clf
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162
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163 def hyperparameter_tuning(self): # Best Params: {'bootstrap': False, 'ccp_alpha': 0.0, 'criterion': 'gini', 'max_features': 'sqrt', 'n_estimators': 250}
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164 from sklearn.model_selection import GridSearchCV
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165 from sklearn.ensemble import RandomForestClassifier
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166 clf = RandomForestClassifier()
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167 n_estimators = [50, 100, 150, 200, 250]
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168 criterion = ['gini', 'entropy']
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169 max_features = ['auto', 'sqrt', 'log2']
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170 bootstrap = [True, False]
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171 ccp_alpha = [0.0, 0.01, 0.02]
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172 param_grid = dict(n_estimators=n_estimators, criterion=criterion, max_features=max_features, bootstrap=bootstrap, ccp_alpha=ccp_alpha)
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173 grid = GridSearchCV(clf, param_grid, n_jobs=-1)
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174 grid_result = grid.fit(self.X_val, self.y_val)
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175 print('Best Score: ', grid_result.best_score_)
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176 print('Best Params: ', grid_result.best_params_)
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177
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178 def __score_metrics(self, method):
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179 from sklearn.metrics import matthews_corrcoef, f1_score, precision_score, recall_score
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180 print(matthews_corrcoef(self.y_test, method.predict(self.X_test)))
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181 print(f1_score(self.y_test, method.predict(self.X_test), average=None))
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182
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183 def __auc_curve(self, method):
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184 import matplotlib.pyplot as plt
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185 from sklearn import metrics
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186 metrics.plot_roc_curve(method, self.X_test, self.y_test)
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187 plt.plot([0, 1], [0, 1], color='navy', lw=2, linestyle='--')
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188 plt.xlim(0, 0.2)
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189 plt.show()
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190
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191 def __plot_roc_cv(self, method, cv):
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192 import numpy as np
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193 import matplotlib.pyplot as plt
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194 from sklearn import datasets
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195 from sklearn.metrics import auc
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196 from sklearn.metrics import plot_roc_curve
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197 tprs = []
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198 aucs = []
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199 mean_fpr = np.linspace(0, 1, 100)
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200 fig, ax = plt.subplots()
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201 for i, (train, test) in enumerate(cv.split(self.data_z, self.output)):
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202 method.fit(self.data_z[train], self.output[train])
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203 viz = plot_roc_curve(method, self.data_z[test], self.output[test], name='ROC fold {}'.format(i), alpha=0.3, lw=1, ax=ax)
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204 interp_tpr = np.interp(mean_fpr, viz.fpr, viz.tpr)
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205 interp_tpr[0] = 0.0
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206 tprs.append(interp_tpr)
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207 aucs.append(viz.roc_auc)
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208 ax.plot([0, 1], [0, 1], linestyle='--', lw=2, color='r', label='Chance', alpha=.8)
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209 mean_tpr = np.mean(tprs, axis=0)
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210 mean_tpr[-1] = 1.0
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211 mean_auc = auc(mean_fpr, mean_tpr)
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212 std_auc = np.std(aucs)
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213 ax.plot(mean_fpr, mean_tpr, color='b', label=r'Mean ROC (AUC = %0.2f $\pm$ %0.2f)' % (mean_auc, std_auc), lw=2, alpha=.8)
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214 std_tpr = np.std(tprs, axis=0)
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215 tprs_upper = np.minimum(mean_tpr + std_tpr, 1)
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216 tprs_lower = np.maximum(mean_tpr - std_tpr, 0)
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217 ax.fill_between(mean_fpr, tprs_lower, tprs_upper, color='grey', alpha=.2, label=r'$\pm$ 1 std. dev.')
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218 ax.set(xlim=[-0.05, 1.05], ylim=[-0.05, 1.05], title="Receiver operating characteristic example")
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219 ax.legend(loc="lower right")
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220 plt.show()
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221
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222 def __permutation_importance(self, method):
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223 from sklearn.inspection import permutation_importance
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224 r = permutation_importance(method, self.X_test, self.y_test, n_repeats=5)
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225 for i in r.importances_mean.argsort()[::-1]:
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226 if r.importances_mean[i] - 2 * r.importances_std[i] > 0.001:
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227 print(f"{self.dataset.columns[i]:<8}"
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228 f" {r.importances_mean[i]:.3f}"
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229 f" +/- {r.importances_std[i]:.3f}")
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230
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231 def recursive_feature_elimination(self, method):
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232 from sklearn.feature_selection import RFECV
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233 selector = RFECV(method, cv=5)#, min_features_to_select=200)
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234 selector.fit(self.data_z, self.output)
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235 print(selector.ranking_)
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236 self.data_reduced = selector.transform(self.data_z)
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237
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238 def predict_interaction(self, phage, bacteria):
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239 from sklearn.svm import LinearSVC
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240 from sklearn.ensemble import RandomForestClassifier
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241 import numpy as np
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242 from feature_construction import FeatureConstruction
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243
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244 phageProts = self.__find_phage_proteins(phage) # dictionary
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245 bactProts = self.__find_bact_proteins(bacteria)
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246 if not phageProts or not bactProts:
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247 print('oops')
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248 return None
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249 list_carb = {}
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250 list_prot = {}
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251 for prot in phageProts.keys():
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252 if any(z in phageProts[prot][0].lower() for z in ['lysin', 'collagen', 'glyco', 'galac', 'chitin', 'wall', 'pectin', 'glycan', 'sialidase', 'neuramin', 'amid', 'lysozyme', 'murami', 'pectate', 'sgnh']):
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253 list_carb[prot] = phageProts[prot]
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254 else:
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255 list_prot[prot] = phageProts[prot]
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256 inter = np.array([])
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257 fc = FeatureConstruction()
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258 grouping = fc.get_grouping(phage=list_prot, phage_carb=list_carb, bacteria=bactProts) # takes a list of protein sequences
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259 inter = np.append(inter, grouping)
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260 composition = fc.get_composition(phage=list_prot, phage_carb=list_carb, bacteria=bactProts)
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261 inter = np.append(inter, composition)
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262 kmers = fc.get_kmers(phage=list_prot, phage_carb=list_carb, bacteria=bactProts)
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263 inter = np.append(inter, kmers)
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264 inter = inter.reshape(1, -1)
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265 inter = self.scaler.transform(inter)
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266 # svm = LinearSVC(C=0.01, tol=0.010, dual=False)
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267 clf = RandomForestClassifier(n_estimators=250, bootstrap=False, ccp_alpha=0.0, max_features='sqrt')
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268 clf = clf.fit(self.data_z, self.output)
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269 pred = clf.predict(inter)[0]
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270 print(pred)
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271 return pred
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272
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273 def __find_phage_proteins(self, phage):
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274 import json
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275 with open('files/phageTails.json', encoding='utf-8') as F:
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276 phageTails = json.loads(F.read())
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277 phageProts = {}
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278 if phage in phageTails.keys():
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279 for prot in phageTails[phage]:
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280 phageProts[prot] = [phageTails[phage][prot][0], phageTails[phage][prot][1]]
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281 else:
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282 from domain_search import DomainSearch
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283 phageProts = self.__find_proteins(phage)
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284 ds = DomainSearch()
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285 phageProts = ds.find_domains_interpro(phageProts)
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286 phageProts = ds.find_domains_blast(phageProts)
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287 phageProts = ds.find_domains_uniprot(phageProts)
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288 return phageProts
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289
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290 def __find_bact_proteins(self, bacteria):
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291 import os
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292 import json
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293 if bacteria + '.json' in os.listdir('files/bacteria'):
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294 with open('files/bacteria/' + bacteria + '.json', encoding='utf-8') as F:
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295 bactProts = json.loads(F.read())
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296 else:
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297 pass
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298 # bactProts = self.__find_proteins(bacteria)
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299 # Implementar previsão de localização celular
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300 return bactProts
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301
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302 def __find_proteins(self, id):
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303 from Bio import Entrez
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304 from Bio import SeqIO
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305 Entrez.email = 'pedro_araujo97@hotmail.com'
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306 prots = {}
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307 with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=id) as handle:
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308 genomeBac = SeqIO.read(handle, "gb")
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309 for feat in genomeBac.features:
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310 if feat.type == 'CDS':
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311 try: prots[feat.qualifiers['protein_id'][0]] = [feat.qualifiers['product'][0], feat.qualifiers['translation'][0]]
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312 except: pass
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313 if len(genomeBac.features) <= 5:
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314 with Entrez.efetch(db="nucleotide", rettype="gbwithparts", retmode="text", id=id) as handle:
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315 genomeBac = handle.readlines()
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316 for i in range(len(genomeBac)):
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317 if ' CDS ' in genomeBac[i]:
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318 j = i
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319 protDone = False
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320 while j < len(genomeBac):
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321 if protDone:
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322 break
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323 if '/product=' in genomeBac[j]:
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324 product = genomeBac[j].strip()[10:]
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325 j += 1
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326 elif '_id=' in genomeBac[j]:
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327 protKey = genomeBac[j].strip()[13:-1]
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328 j += 1
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329 elif '/translation=' in genomeBac[j]:
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330 protSeq = genomeBac[j].strip()[14:]
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331 j += 1
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332 for k in range(j, len(genomeBac)):
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333 if genomeBac[k].islower():
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334 j = k
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335 protDone = True
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336 break
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337 else:
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338 protSeq += genomeBac[k].strip()
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339 else:
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340 j += 1
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341 prots[protKey] = [product, protSeq[:protSeq.find('"')]]
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342 return prots
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343
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344
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345 if __name__ == '__main__':
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346 ml = PredictInteraction('dataset_reduced') # FeatureDataset
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347 # ml.predict_interaction('NC_050143', 'NC_020524.1') # NC_010468.1 NC_013941.1 NZ_CP029060.1 NZ_CP027394.1 NZ_CP025089.1
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348 ml.predict_interaction('KM607000', 'NC_020524') # NC_010468.1 NC_013941.1 NZ_CP029060.1 NZ_CP027394.1 NZ_CP025089.1
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349 ml.run_knn(2)
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350 ml.run_random_forest()
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351 ml.run_svm(0.001)
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352 ml.run_neural_networks(0.0001)
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353 ml.run_logistic_reg(0.01)
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354
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355 import pandas as pd
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356 import ast
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357 data = pd.read_csv('files/NCBI_Phage_Bacteria_Data.csv', header=0, index_col=0)
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358 abaumannii = {}
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359 for phage in data.index:
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360 name = data.loc[phage, 'Host']
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361 if 'acinetobacter' in name.lower():
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362 for bact in ast.literal_eval(data.loc[phage, 'Host_ID']):
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363 abaumannii[bact] = 0
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364 list_yes = {}
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365 list_yes['KT588074'] = []
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366 for bact in abaumannii.keys():
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367 predict = ml.predict_interaction('KT588074', bact)
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368 if predict == 'Yes':
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369 list_yes['KT588074'].append(bact)
|
