loopity_loop_CALL
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5 changed files with 163 additions and 188 deletions
163
imports.py
163
imports.py
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@ -27,6 +27,8 @@ from sklearn.metrics import roc_auc_score, roc_curve, f1_score, matthews_corrcoe
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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.metrics import average_precision_score
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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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@ -43,6 +45,16 @@ 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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from imblearn.over_sampling import RandomOverSampler
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from imblearn.over_sampling import SMOTE
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from imblearn.pipeline import Pipeline
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#from sklearn.datasets import make_classification
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from sklearn.model_selection import cross_validate
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from sklearn.model_selection import RepeatedStratifiedKFold
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from sklearn.ensemble import AdaBoostClassifier
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from imblearn.combine import SMOTEENN
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from imblearn.under_sampling import EditedNearestNeighbours
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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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@ -52,8 +64,8 @@ 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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gene = 'pncA'
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drug = 'pyrazinamide'
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#==============
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# directories
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@ -79,64 +91,33 @@ 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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# change from numberic to
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num_type = ['int64', 'float64']
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cat_type = ['object', 'bool']
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if my_df['active_aa_pos'].dtype in num_type:
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my_df['active_aa_pos'] = my_df['active_aa_pos'].astype(object)
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my_df['active_aa_pos'].dtype
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# FIXME: if this is not structural, remove from source..
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# Drop NA where numerical cols have them
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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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# FIXME: either impute or remove!
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# for embb (L114M, F115L, V123L, V125I, V131M) delete for now
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if gene.lower() in ['embb']:
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na_index = my_df['mutationinformation'].index[my_df['ligand_distance'].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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# Target1: mutation_info_labels, convert to
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dm_om_map = {'DM': 1, 'OM': 0} # pnca, OM is minority, other genes: DM is minority
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my_df['mutation_class'] = my_df['mutation_info_labels'].map(dm_om_map)
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my_df['mutation_class'].value_counts()
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my_df['mutation_info_labels']. value_counts()
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#%%
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# GET X
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@ -159,10 +140,7 @@ if gene.lower() in geneL_na:
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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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@ -172,53 +150,48 @@ 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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#%% Construct numerical and categorical column names
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numerical_FN = 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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categorical_FN = ['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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#%% extracting dfs based on numerical, categorical column names
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#----------------------------------
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# WITHOUT the target var included
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#----------------------------------
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num_df = my_df[numerical_FN]
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num_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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cat_df = my_df[categorical_FN]
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cat_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
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all_df = my_df[numerical_FN + categorical_FN]
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all_df.shape
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#------------------------------
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# WITH the target var included:
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#'wtgt': with target
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#------------------------------
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num_df_wtgt = my_df[numerical_FN + ['mutation_class']]
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num_df_wtgt.shape
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cat_df_wtgt = my_df[categorical_FN + ['mutation_class']]
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cat_df_wtgt.shape
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all_df_wtgt = my_df[numerical_FN + categorical_FN + ['mutation_class']]
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all_df_wtgt.shape
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