224 lines
No EOL
7.2 KiB
Python
224 lines
No EOL
7.2 KiB
Python
#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Sun Mar 6 13:41:54 2022
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@author: tanu
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"""
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import os, sys
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import pandas as pd
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import numpy as np
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from sklearn import linear_model
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from sklearn.linear_model import LogisticRegression, LinearRegression
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from sklearn.naive_bayes import BernoulliNB
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from sklearn.neighbors import KNeighborsClassifier
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from sklearn.svm import SVC
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from sklearn.tree import DecisionTreeClassifier
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from sklearn.ensemble import RandomForestClassifier, ExtraTreesClassifier
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from sklearn.neural_network import MLPClassifier
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from xgboost import XGBClassifier
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from sklearn.preprocessing import StandardScaler, MinMaxScaler, OneHotEncoder
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from sklearn.compose import ColumnTransformer
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from sklearn.compose import make_column_transformer
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from sklearn.metrics import confusion_matrix, accuracy_score, precision_score, recall_score
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from sklearn.metrics import roc_auc_score, roc_curve, f1_score, matthews_corrcoef
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from sklearn.metrics import make_scorer
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from sklearn.metrics import classification_report
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from sklearn.model_selection import cross_validate
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from sklearn.model_selection import train_test_split
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from sklearn.model_selection import StratifiedKFold
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from sklearn.pipeline import Pipeline
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from sklearn.pipeline import make_pipeline
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from sklearn.feature_selection import RFE
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from sklearn.feature_selection import RFECV
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import itertools
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import seaborn as sns
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import matplotlib.pyplot as plt
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import numpy as np
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print(np.__version__)
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print(pd.__version__)
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from statistics import mean, stdev, median, mode
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#%%
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homedir = os.path.expanduser("~")
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os.chdir(homedir + "/git/ML_AI_training/")
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# my function
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from MultClassPipe import MultClassPipeline
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from MultClassPipe2 import MultClassPipeline2
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from loopity_loop import MultClassPipeSKF
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gene = 'rpoB'
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drug = 'rifampicin'
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#==============
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# directories
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#==============
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datadir = homedir + '/git/Data/'
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indir = datadir + drug + '/input/'
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outdir = datadir + drug + '/output/'
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#=======
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# input
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#=======
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infile_ml1 = outdir + gene.lower() + '_merged_df3.csv'
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#infile_ml2 = outdir + gene.lower() + '_merged_df2.csv'
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my_df = pd.read_csv(infile_ml1)
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my_df.dtypes
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my_df_cols = my_df.columns
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geneL_basic = ['pnca']
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geneL_na = ['gid']
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geneL_na_ppi2 = ['rpob']
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geneL_ppi2 = ['alr', 'embb', 'katg']
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#%% get cols
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mycols = my_df.columns
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my_df['active_aa_pos'].dtype
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my_df['active_aa_pos'] = my_df['active_aa_pos'].astype(object)
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if gene.lower() in geneL_na_ppi2:
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x_stabilityN = common_cols_stabiltyN + ['mcsm_na_affinity'] + ['mcsm_ppi2_affinity', 'interface_dist']
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#D1148 get rid of
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na_index = my_df['mutationinformation'].index[my_df['mcsm_na_affinity'].apply(np.isnan)]
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my_df = my_df.drop(index=na_index)
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#%%============================================================================
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# GET Y
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# Target1: mutation_info_labels
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dm_om_map = {'DM': 1, 'OM': 0}
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target1 = my_df['mutation_info_labels'].map(dm_om_map)
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target1.value_counts()
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# Target2: drug
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drug_labels = drug + '_labels'
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drug_labels
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my_df[drug_labels] = my_df[drug].map({1: 'resistant', 0: 'sensitive'})
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my_df[drug_labels].value_counts()
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my_df[drug_labels] = my_df[drug_labels].fillna('unknown')
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my_df[drug_labels].value_counts()
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target2 = my_df[drug_labels]
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# Target3: drtype [Binary]
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drtype_labels = 'drtype_labels'
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my_df[drtype_labels] = my_df['drtype'].map({'Sensitive' : 0
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, 'Other' : 0
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, 'Pre-MDR' : 1
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, 'MDR' : 1
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, 'Pre-XDR' : 1
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, 'XDR' : 1})
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# target3 = 'drtype' [Multinomial]
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target3 = my_df[drtype_labels]
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# target4
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drtype_labels2 = 'drtype_labels2'
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my_df[drtype_labels2] = my_df['drtype'].map({'Sensitive' : 0
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, 'Other' : 0
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, 'Pre-MDR' : 1
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, 'MDR' : 1
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, 'Pre-XDR' : 2
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, 'XDR' : 2})
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target4 = my_df[drtype_labels2]
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# sanity checks
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target1.value_counts()
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my_df['mutation_info_labels'].value_counts()
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target2.value_counts()
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my_df[drug_labels].value_counts()
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target3.value_counts()
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my_df['drtype'].value_counts()
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target4.value_counts()
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my_df['drtype'].value_counts()
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#%%
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# GET X
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common_cols_stabiltyN = ['ligand_distance'
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, 'ligand_affinity_change'
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, 'duet_stability_change'
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, 'ddg_foldx'
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, 'deepddg'
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, 'ddg_dynamut2']
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# Build stability columns ~ gene
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if gene.lower() in geneL_basic:
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x_stabilityN = common_cols_stabiltyN
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if gene.lower() in geneL_ppi2:
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x_stabilityN = common_cols_stabiltyN + ['mcsm_ppi2_affinity'
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, 'interface_dist']
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if gene.lower() in geneL_na:
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x_stabilityN = common_cols_stabiltyN + ['mcsm_na_affinity']
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if gene.lower() in geneL_na_ppi2:
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x_stabilityN = common_cols_stabiltyN + ['mcsm_na_affinity'] + ['mcsm_ppi2_affinity', 'interface_dist']
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#D1148 get rid of
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na_index = my_df['mutationinformation'].index[my_df['mcsm_na_affinity'].apply(np.isnan)]
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my_df = my_df.drop(index=na_index)
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X_strFN = ['asa'
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, 'rsa'
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, 'kd_values'
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, 'rd_values']
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X_evolFN = ['consurf_score'
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, 'snap2_score'
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, 'snap2_accuracy_pc']
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# TODO: ADD ED values
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# Problematic due to NA: filling NA with unknown or string will make it categorical
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# OPTIONS
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# 1. Imputing: KNN or MICE or from distribution
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# 2. Fill na with median or mode
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# 3. Separate datset without including genomic features AT ALL for ML, then using this as a 'blind test set'
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# this means the size of the training data gets reduced!
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# 4. Remove genomic features from ML COMPLETELEY!
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# X_genomicFN = ['af'
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# , 'or_mychisq'
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# , 'or_logistic'
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# , 'or_fisher'
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# , 'pval_fisher']
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#%% try combinations
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X_vars1 = my_df[x_stabilityN]
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X_vars2 = my_df[X_strFN]
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X_vars3 = my_df[X_evolFN]
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X_vars5 = my_df[x_stabilityN + X_strFN]
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X_vars6 = my_df[x_stabilityN + X_evolFN]
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#X_vars7 = my_df[x_stabilityN + X_genomicFN]
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X_vars8 = my_df[X_strFN + X_evolFN]
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#X_vars9 = my_df[X_strFN + X_genomicFN]
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#X_vars10 = my_df[X_evolFN + X_genomicFN]
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X_vars11 = my_df[x_stabilityN + X_strFN + X_evolFN]
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#X_vars12 = my_df[x_stabilityN + X_strFN + X_evolFN + X_genomicFN]
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numerical_features_names = x_stabilityN + X_strFN + X_evolFN
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# separate ones for foldx?
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categorical_features_names = ['ss_class'
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, 'wt_prop_water'
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# , 'lineage_labels' # misleading if using merged_df3
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, 'mut_prop_water'
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, 'wt_prop_polarity'
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, 'mut_prop_polarity'
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, 'wt_calcprop'
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, 'mut_calcprop'
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, 'active_aa_pos']
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numerical_features_df = my_df[numerical_features_names]
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numerical_features_df.shape
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categorical_features_df = my_df[categorical_features_names]
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categorical_features_df.shape
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all_features_df = my_df[numerical_features_names + categorical_features_names]
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all_features_df.shape |