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tidying script to run from cmd and via ssh

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Tanushree Tunstall 2022-05-28 09:40:24 +01:00
parent 0a84a4b4dc
commit b6f0308e42
4 changed files with 271 additions and 76 deletions
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UQ_pnca_ML.py
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@ -10,77 +10,57 @@ Created on Sun Mar 6 13:41:54 2022
import os, sys
import pandas as pd
import numpy as np
print(np.__version__)
print(pd.__version__)
import pprint as pp
from copy import deepcopy
from sklearn import linear_model
from sklearn import datasets
from collections import Counter
from sklearn.linear_model import LogisticRegression, LinearRegression
from sklearn.linear_model import LogisticRegression, LogisticRegressionCV
from sklearn.linear_model import RidgeClassifier, RidgeClassifierCV, SGDClassifier, PassiveAggressiveClassifier
from sklearn.naive_bayes import BernoulliNB
from sklearn.neighbors import KNeighborsClassifier
from sklearn.svm import SVC
from sklearn.tree import DecisionTreeClassifier
from sklearn.ensemble import RandomForestClassifier, ExtraTreesClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.tree import DecisionTreeClassifier, ExtraTreeClassifier
from sklearn.ensemble import RandomForestClassifier, ExtraTreesClassifier, AdaBoostClassifier, GradientBoostingClassifier, BaggingClassifier
from sklearn.naive_bayes import GaussianNB
from sklearn.gaussian_process import GaussianProcessClassifier
from sklearn.gaussian_process import kernels
from sklearn.gaussian_process.kernels import RBF
from sklearn.gaussian_process.kernels import DotProduct
from sklearn.gaussian_process.kernels import Matern
from sklearn.gaussian_process.kernels import RationalQuadratic
from sklearn.gaussian_process.kernels import WhiteKernel
from sklearn.gaussian_process import GaussianProcessClassifier, kernels
from sklearn.gaussian_process.kernels import RBF, DotProduct, Matern, RationalQuadratic, WhiteKernel
from sklearn.discriminant_analysis import QuadraticDiscriminantAnalysis
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis, QuadraticDiscriminantAnalysis
from sklearn.neural_network import MLPClassifier
from sklearn.linear_model import RidgeClassifier, SGDClassifier, PassiveAggressiveClassifier
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from sklearn.svm import SVC
from xgboost import XGBClassifier
from sklearn.naive_bayes import MultinomialNB
from sklearn.linear_model import SGDClassifier
from sklearn.preprocessing import StandardScaler, MinMaxScaler, OneHotEncoder
from sklearn.compose import ColumnTransformer
from sklearn.compose import make_column_transformer
from sklearn.metrics import confusion_matrix, accuracy_score, precision_score, recall_score
from sklearn.metrics import roc_auc_score, roc_curve, f1_score, matthews_corrcoef, jaccard_score
from sklearn.metrics import jaccard_score
from sklearn.metrics import make_scorer
from sklearn.metrics import classification_report
from sklearn.metrics import make_scorer, confusion_matrix, accuracy_score, balanced_accuracy_score, precision_score, average_precision_score, recall_score
from sklearn.metrics import roc_auc_score, roc_curve, f1_score, matthews_corrcoef, jaccard_score, classification_report
from sklearn.metrics import average_precision_score
from sklearn.model_selection import train_test_split, cross_validate, cross_val_score
from sklearn.model_selection import StratifiedKFold,RepeatedStratifiedKFold, RepeatedKFold
from sklearn.model_selection import cross_validate
from sklearn.model_selection import train_test_split
from sklearn.model_selection import StratifiedKFold
from sklearn.pipeline import Pipeline, make_pipeline
from sklearn.pipeline import Pipeline
from sklearn.pipeline import make_pipeline
from sklearn.feature_selection import RFE, RFECV
from sklearn.feature_selection import RFE
from sklearn.feature_selection import RFECV
import itertools
#import seaborn as sns
import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np
print(np.__version__)
print(pd.__version__)
from statistics import mean, stdev, median, mode
from imblearn.over_sampling import RandomOverSampler
from imblearn.under_sampling import RandomUnderSampler
from imblearn.over_sampling import SMOTE
from imblearn.pipeline import Pipeline
from sklearn.datasets import make_classification
from sklearn.model_selection import cross_validate, cross_val_score
from sklearn.model_selection import RepeatedStratifiedKFold
from sklearn.ensemble import AdaBoostClassifier
from imblearn.combine import SMOTEENN
from imblearn.combine import SMOTETomek
@ -124,8 +104,8 @@ os.chdir(homedir + "/git/ML_AI_training/")
from MultClassPipe2 import MultClassPipeline2
from loopity_loop import MultClassPipeSKFLoop
#from MultClassPipe3 import MultClassPipeSKFCV
from UQ_MultClassPipe4 import MultClassPipeSKFCV
#from UQ_MultClassPipe4 import MultClassPipeSKFCV
from UQ_MultModelsCl import MultModelsCl
#gene = 'pncA'
#drug = 'pyrazinamide'