optimised run_7030.py to generate ouput from dict now that the processfunction and parameter dicts have been added
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12 changed files with 180 additions and 128408 deletions
635
scripts/ml/run_7030.py
Executable file → Normal file
635
scripts/ml/run_7030.py
Executable file → Normal file
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@ -5,28 +5,28 @@ Created on Mon Jun 20 13:05:23 2022
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@author: tanu
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"""
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#%%Imports ####################################################################
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import re
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import argparse
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###############################################################################
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import os, sys
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# gene = 'pncA'
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# drug = 'pyrazinamide'
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#total_mtblineage_uc = 8
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###############################################################################
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#%% command line args: case sensitive
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arg_parser = argparse.ArgumentParser()
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arg_parser.add_argument('-d', '--drug', help = 'drug name', default = '')
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arg_parser.add_argument('-g', '--gene', help = 'gene name', default = '')
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args = arg_parser.parse_args()
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# arg_parser = argparse.ArgumentParser()
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# arg_parser.add_argument('-d', '--drug', help = 'drug name', default = '')
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# arg_parser.add_argument('-g', '--gene', help = 'gene name', default = '')
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# args = arg_parser.parse_args()
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drug = args.drug
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gene = args.gene
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# drug = args.drug
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# gene = args.gene
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###############################################################################
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#==================
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# other vars
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#==================
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tts_split = '70/30'
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OutFile_suffix = '7030'
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homedir = os.path.expanduser("~")
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sys.path.append(homedir + '/git/LSHTM_analysis/scripts/ml')
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###############################################################################
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#==================
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# Import data
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@ -39,10 +39,15 @@ from ml_data_7030 import *
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#from UQ_yc_RunAllClfs import run_all_ML
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#====================
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# Import ML function
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# Import ML functions
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#====================
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# TT run all ML clfs: baseline model
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from MultModelsCl import MultModelsCl
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from MultClfs import *
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#==================
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# other vars
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#==================
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tts_split_7030 = '70_30'
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OutFile_suffix = '7030'
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#==================
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# Specify outdir
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@ -51,563 +56,71 @@ outdir_ml = outdir + 'ml/tts_7030/'
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print('\nOutput directory:', outdir_ml)
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outFile_wf = outdir_ml + gene.lower() + '_baselineC_' + OutFile_suffix + '.csv'
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outFile_lf = outdir_ml + gene.lower() + '_baselineC_ext_' + OutFile_suffix + '.csv'
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#outFile_lf = outdir_ml + gene.lower() + '_baselineC_ext_' + OutFile_suffix + '.csv'
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###############################################################################
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score_type_ordermapD = { 'mcc' : 1
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, 'fscore' : 2
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, 'jcc' : 3
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, 'precision' : 4
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, 'recall' : 5
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, 'accuracy' : 6
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, 'roc_auc' : 7
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, 'TN' : 8
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, 'FP' : 9
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, 'FN' : 10
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, 'TP' : 11
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, 'trainingY_neg': 12
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, 'trainingY_pos': 13
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, 'blindY_neg' : 14
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, 'blindY_pos' : 15
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, 'fit_time' : 16
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, 'score_time' : 17
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}
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scoreCV_mapD = {'test_mcc' : 'MCC'
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, 'test_fscore' : 'F1'
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, 'test_precision' : 'Precision'
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, 'test_recall' : 'Recall'
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, 'test_accuracy' : 'Accuracy'
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, 'test_roc_auc' : 'ROC_AUC'
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, 'test_jcc' : 'JCC'
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}
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scoreBT_mapD = {'bts_mcc' : 'MCC'
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, 'bts_fscore' : 'F1'
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, 'bts_precision' : 'Precision'
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, 'bts_recall' : 'Recall'
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, 'bts_accuracy' : 'Accuracy'
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, 'bts_roc_auc' : 'ROC_AUC'
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, 'bts_jcc' : 'JCC'
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}
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# data dependent variables but NOT dependent on resampling
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bts_size = len(X_bts)
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yc2 = Counter(y_bts)
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yc2_ratio = yc2[0]/yc2[1]
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###############################################################################
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#%% Running models ############################################################
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print('\n#####################################################################\n'
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, '\nRunning ML analysis: feature groups '
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, '\nStarting--> Running ML analysis: Baseline modes (No FS)'
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, '\nGene name:', gene
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, '\nDrug name:', drug)
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, '\nDrug name:', drug
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, '\n#####################################################################\n')
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#%% Basic: No Oversampling
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#================
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# Baseline
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# No resampling
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#================
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scores_mmD = MultModelsCl(input_df = X
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, target = y
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, var_type = 'mixed'
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, skf_cv = skf_cv
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, blind_test_df = X_bts
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, blind_test_target = y_bts
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, add_cm = True
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, add_yn = True)
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baseline_all_scores = pd.DataFrame(scores_mmD)
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rs_none = 'none'
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#------------------------
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# WF: only CV and BTS
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#-----------------------
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baseline_allT = baseline_all_scores.T
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#baseline_train = baseline_all.filter(regex='train_', axis=1)
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baseline_CV = baseline_allT.filter(regex='test_', axis = 1); baseline_CV.columns
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# map colnames for consistency to allow concatenting
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baseline_CV.columns = baseline_CV.columns.map(scoreCV_mapD); baseline_CV.columns
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baseline_CV['Data_source'] = 'CV'
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baseline_CV['Resampling'] = rs_none
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baseline_BT = baseline_allT.filter(regex='bts_', axis = 1); baseline_BT.columns
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# map colnames for consistency to allow concatenting
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baseline_BT.columns = baseline_BT.columns.map(scoreBT_mapD); baseline_BT.columns
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baseline_BT['Data_source'] = 'BT'
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baseline_BT['Resampling'] = rs_none
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# # Write csv
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#baseline_CV.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
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#baseline_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
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# baseline_CV.to_csv(outdir_ml + gene.lower() + '_baseline_CV_allF.csv')
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# baseline_BT.to_csv(outdir_ml + gene.lower() + '_baseline_BT_allF.csv')
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#----------------------------------
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# LF*: CV + BTS + Other info
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#-----------------------------------
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# other data dependent variables
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training_size_ns = len(X)
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n_features = len(X.columns)
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yc1 = Counter(y)
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yc1_ratio = yc1[0]/yc1[1]
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baseline_all = baseline_all_scores.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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baseline_all = baseline_all.reset_index()
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baseline_all.rename(columns = {'index': 'original_names'}, inplace = True)
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# Indicate whether BT or CV
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bt_pattern = re.compile(r'bts_.*')
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baseline_all['Data_source'] = baseline_all.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
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baseline_all['score_type'] = baseline_all['original_names'].str.replace('bts_|test_', '', regex = True)
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score_type_uniqueN = set(baseline_all['score_type'])
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cL1 = list(score_type_ordermapD.keys())
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cL2 = list(score_type_uniqueN)
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if set(cL1).issubset(cL2):
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print('\nPASS: sorting df by score that is mapped onto the order I want')
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baseline_all['score_order'] = baseline_all['score_type'].map(score_type_ordermapD)
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baseline_all.sort_values(by = ['Data_source', 'score_order'], ascending = [True, True], inplace = True)
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else:
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sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
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# add cols: specific
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baseline_all['Resampling'] = rs_none
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baseline_all['training_size'] = training_size_ns
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baseline_all['trainingY_ratio']= round(yc1_ratio,2)
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baseline_all['n_features'] = n_features
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###############################################################################
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#%% SMOTE NC: Smote Oversampling [Numerical + categorical]
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#================
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# Baseline
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# SMOTE NC: SMNC
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#================
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smnc_scores_mmD = MultModelsCl(input_df = X_smnc
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, target = y_smnc
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, var_type = 'mixed'
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, skf_cv = skf_cv
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, blind_test_df = X_bts
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, blind_test_target = y_bts
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, add_cm = True
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, add_yn = True)
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smnc_all_scores = pd.DataFrame(smnc_scores_mmD)
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rs_smnc = 'smnc'
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#------------------------
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# WF: only CV and BTS
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#-----------------------
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smnc_allT = smnc_all_scores.T
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smnc_CV = smnc_allT.filter(regex='test_', axis = 1); smnc_CV.columns
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# map colnames for consistency to allow concatenting
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smnc_CV.columns = smnc_CV.columns.map(scoreCV_mapD); smnc_CV.columns
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smnc_CV['Data_source'] = 'CV'
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smnc_CV['Resampling'] = rs_smnc
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smnc_BT = smnc_allT.filter(regex='bts_', axis = 1); smnc_BT.columns
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# map colnames for consistency to allow concatenting
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smnc_BT.columns = smnc_BT.columns.map(scoreBT_mapD); smnc_BT.columns
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smnc_BT['Data_source'] = 'BT'
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smnc_BT['Resampling'] = rs_smnc
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# Write csv
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# smnc_CV.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
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# smnc_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
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# smnc_CV.to_csv(outdir_ml + gene.lower() + '_smnc_CV_allF.csv')
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# smnc_BT.to_csv(outdir_ml + gene.lower() + '_smnc_BT_allF.csv')
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#----------------------------------
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# LF*: CV + BTS + Other info
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#-----------------------------------
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# other data dependent variables
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training_size_smnc = len(X_smnc)
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n_features = len(X_smnc.columns)
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yc1_smnc = Counter(y_smnc)
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yc1_ratio_smnc = yc1_smnc[0]/yc1_smnc[1]
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smnc_all = smnc_all_scores.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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smnc_all = smnc_all.reset_index()
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smnc_all.rename(columns = {'index': 'original_names'}, inplace = True)
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# Indicate whether BT or CV
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bt_pattern = re.compile(r'bts_.*')
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smnc_all['Data_source'] = smnc_all.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
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smnc_all['score_type'] = smnc_all['original_names'].str.replace('bts_|test_', '', regex = True)
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score_type_uniqueN = set(smnc_all['score_type'])
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cL1 = list(score_type_ordermapD.keys())
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cL2 = list(score_type_uniqueN)
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if set(cL1).issubset(cL2):
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print('\nPASS: sorting df by score that is mapped onto the order I want')
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smnc_all['score_order'] = smnc_all['score_type'].map(score_type_ordermapD)
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smnc_all.sort_values(by = ['Data_source', 'score_order'], ascending = [True, True], inplace = True)
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else:
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sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
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# add cols: specific
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smnc_all['Resampling'] = rs_smnc
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smnc_all['training_size'] = training_size_smnc
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smnc_all['trainingY_ratio'] = round(yc1_ratio_smnc,2)
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smnc_all['n_features'] = n_features
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###############################################################################
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#%% ROS: Random Over Sampling [Numerical + categorical]
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#================
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# Baseline
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# ROS
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#================
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ros_scores_mmD = MultModelsCl(input_df = X_ros
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, target = y_ros
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, var_type = 'mixed'
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, skf_cv = skf_cv
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, blind_test_df = X_bts
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, blind_test_target = y_bts
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, add_cm = True
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, add_yn = True)
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ros_all_scores = pd.DataFrame(ros_scores_mmD)
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rs_ros = 'ros'
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#------------------------
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# WF: only CV and BTS
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#-----------------------
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ros_allT = ros_all_scores.T
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ros_CV = ros_allT.filter(regex='test_', axis = 1); ros_CV.columns
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# map colnames for consistency to allow concatenting
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ros_CV.columns = ros_CV.columns.map(scoreCV_mapD); ros_CV.columns
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ros_CV['Data_source'] = 'CV'
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ros_CV['Resampling'] = rs_ros
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ros_BT = ros_allT.filter(regex='bts_', axis = 1); ros_BT.columns
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# map colnames for consistency to allow concatenting
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ros_BT.columns = ros_BT.columns.map(scoreBT_mapD); ros_BT.columns
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ros_BT['Data_source'] = 'BT'
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ros_BT['Resampling'] = rs_ros
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# Write csv
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# ros_CV.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
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# ros_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
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# ros_CV.to_csv(outdir_ml + gene.lower() + '_ros_CV_allF.csv')
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# ros_BT.to_csv(outdir_ml + gene.lower() + '_ros_BT_allF.csv')
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#----------------------------------
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# LF*: CV + BTS + Other info
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#----------------------------------
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# other data dependent variables
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training_size_ros = len(X_ros)
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n_features = len(X_ros.columns)
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yc1_ros = Counter(y_ros)
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yc1_ratio_ros = yc1_ros[0]/yc1_ros[1]
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ros_all = ros_all_scores.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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ros_all = ros_all.reset_index()
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ros_all.rename(columns = {'index': 'original_names'}, inplace = True)
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# Indicate whether BT or CV
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bt_pattern = re.compile(r'bts_.*')
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ros_all['Data_source'] = ros_all.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
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ros_all['score_type'] = ros_all['original_names'].str.replace('bts_|test_', '', regex = True)
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score_type_uniqueN = set(ros_all['score_type'])
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cL1 = list(score_type_ordermapD.keys())
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cL2 = list(score_type_uniqueN)
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if set(cL1).issubset(cL2):
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print('\nPASS: sorting df by score that is mapped onto the order I want')
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ros_all['score_order'] = ros_all['score_type'].map(score_type_ordermapD)
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ros_all.sort_values(by = ['Data_source', 'score_order'], ascending = [True, True], inplace = True)
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else:
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sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
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# add cols: specific
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ros_all['Resampling'] = rs_ros
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ros_all['training_size'] = training_size_ros
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ros_all['trainingY_ratio'] = round(yc1_ratio_ros,2)
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ros_all['n_features'] = n_features
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###############################################################################
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#%% RUS: Random Under Sampling [Numerical + categorical]
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#================
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# Baseline
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# RUS
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#================
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rus_scores_mmD = MultModelsCl(input_df = X_rus
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, target = y_rus
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, var_type = 'mixed'
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, skf_cv = skf_cv
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, blind_test_df = X_bts
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, blind_test_target = y_bts
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, add_cm = True
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, add_yn = True)
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rus_all_scores = pd.DataFrame(rus_scores_mmD)
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rs_rus = 'rus'
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#-----------------------
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# WF: only CV and BTS
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#-----------------------
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rus_allT = rus_all_scores.T
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rus_CV = rus_allT.filter(regex='test_', axis=1); rus_CV.columns
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# map colnames for consistency to allow concatenting
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rus_CV.columns = rus_CV.columns.map(scoreCV_mapD); rus_CV.columns
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rus_CV['Data_source'] = 'CV'
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rus_CV['Resampling'] = rs_rus
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rus_BT = rus_allT.filter(regex='bts_' , axis=1); rus_BT.columns
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# map colnames for consistency to allow concatenting
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rus_BT.columns = rus_BT.columns.map(scoreBT_mapD); rus_BT.columns
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rus_BT['Data_source'] = 'BT'
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rus_BT['Resampling'] = rs_rus
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# # Write csv
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# rus_CV.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
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# rus_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
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# rus_CV.to_csv(outdir_ml + gene.lower() + '_rus_CV_allF.csv')
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# rus_BT.to_csv(outdir_ml + gene.lower() + '_rus_BT_allF.csv')
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#----------------------------------
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# LF*: CV + BTS + Other info
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#----------------------------------
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# other data dependent variables
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training_size_rus = len(X_rus)
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n_features = len(X_rus.columns)
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yc1_rus = Counter(y_rus)
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yc1_ratio_rus = yc1_rus[0]/yc1_rus[1]
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rus_all = rus_all_scores.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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rus_all = rus_all.reset_index()
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rus_all.rename(columns = {'index': 'original_names'}, inplace = True)
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# Indicate whether BT or CV
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bt_pattern = re.compile(r'bts_.*')
|
||||
rus_all['Data_source'] = rus_all.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||
|
||||
rus_all['score_type'] = rus_all['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||
|
||||
score_type_uniqueN = set(rus_all['score_type'])
|
||||
cL1 = list(score_type_ordermapD.keys())
|
||||
cL2 = list(score_type_uniqueN)
|
||||
|
||||
if set(cL1).issubset(cL2):
|
||||
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||
rus_all['score_order'] = rus_all['score_type'].map(score_type_ordermapD)
|
||||
rus_all.sort_values(by = ['Data_source', 'score_order'], ascending = [True, True], inplace = True)
|
||||
else:
|
||||
sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
|
||||
|
||||
# add cols: specific
|
||||
rus_all['Resampling'] = rs_rus
|
||||
rus_all['training_size'] = training_size_rus
|
||||
rus_all['trainingY_ratio'] = round(yc1_ratio_rus,2)
|
||||
rus_all['n_features'] = n_features
|
||||
|
||||
###############################################################################
|
||||
#%% ROS+RUS Combined: [Numerical + categorical]
|
||||
#================
|
||||
# Baseline
|
||||
# ROUC
|
||||
#================
|
||||
rouC_scores_mmD = MultModelsCl(input_df = X_rouC
|
||||
, target = y_rouC
|
||||
, var_type = 'mixed'
|
||||
, skf_cv = skf_cv
|
||||
, blind_test_df = X_bts
|
||||
, blind_test_target = y_bts
|
||||
, add_cm = True
|
||||
, add_yn = True)
|
||||
|
||||
rouC_all_scores = pd.DataFrame(rouC_scores_mmD)
|
||||
rs_rouC = 'rouC'
|
||||
#-----------------------
|
||||
# WF: only CV and BTS
|
||||
#-----------------------
|
||||
rouC_allT = rouC_all_scores.T
|
||||
|
||||
rouC_CV = rouC_allT.filter(regex='test_', axis=1); rouC_CV.columns
|
||||
# map colnames for consistency to allow concatenting
|
||||
rouC_CV.columns = rouC_CV.columns.map(scoreCV_mapD); rouC_CV.columns
|
||||
rouC_CV['Data_source'] = 'CV'
|
||||
rouC_CV['Resampling'] = rs_rouC
|
||||
|
||||
rouC_BT = rouC_allT.filter(regex='bts_', axis=1); rouC_BT.columns
|
||||
# map colnames for consistency to allow concatenting
|
||||
rouC_BT.columns = rouC_BT.columns.map(scoreBT_mapD); rouC_BT.columns
|
||||
rouC_BT['Data_source'] = 'BT'
|
||||
rouC_BT['Resampling'] = rs_rouC
|
||||
|
||||
# Write csv
|
||||
# rouC_CV.sort_values(by = ['test_mcc'], ascending = False, inplace = True)
|
||||
# rouC_CV.to_csv(outdir_ml + gene.lower() + '_rouC_CV_allF.csv')
|
||||
# rouC_BT.sort_values(by = ['bts_mcc'], ascending = False, inplace = True)
|
||||
# rouC_BT.to_csv(outdir_ml + gene.lower() + '_rouC_BT_allF.csv')
|
||||
|
||||
#----------------------------------
|
||||
# LF*: CV + BTS + Other info
|
||||
#----------------------------------
|
||||
# other data dependent variables
|
||||
training_size_rouC = len(X_rouC)
|
||||
n_features = len(X_rouC.columns)
|
||||
yc1_rouC = Counter(y_rouC)
|
||||
yc1_ratio_rouC = yc1_rouC[0]/yc1_rouC[1]
|
||||
|
||||
rouC_all = rouC_all_scores.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||
rouC_all = rouC_all.reset_index()
|
||||
rouC_all.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||
|
||||
# Indicate whether BT or CV
|
||||
bt_pattern = re.compile(r'bts_.*')
|
||||
rouC_all['Data_source'] = rouC_all.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||
|
||||
rouC_all['score_type'] = rouC_all['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||
|
||||
score_type_uniqueN = set(rouC_all['score_type'])
|
||||
cL1 = list(score_type_ordermapD.keys())
|
||||
cL2 = list(score_type_uniqueN)
|
||||
|
||||
if set(cL1).issubset(cL2):
|
||||
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||
rouC_all['score_order'] = rouC_all['score_type'].map(score_type_ordermapD)
|
||||
rouC_all.sort_values(by = ['Data_source', 'score_order'], ascending = [True, True], inplace = True)
|
||||
else:
|
||||
sys.exit('\nFAIL: could not sort df as score mapping for ordering failed')
|
||||
|
||||
# add cols: specific
|
||||
rouC_all['Resampling'] = rs_rouC
|
||||
rouC_all['training_size'] = training_size_rouC
|
||||
rouC_all['trainingY_ratio'] = round(yc1_ratio_rouC,2)
|
||||
rouC_all['n_features'] = n_features
|
||||
|
||||
###############################################################################
|
||||
#%% COMBINING all dfs: WF and LF
|
||||
# https://stackoverflow.com/questions/39862654/pandas-concat-of-multiple-data-frames-using-only-common-columns
|
||||
#%% Combine WF
|
||||
#-----------------
|
||||
# Combine WF
|
||||
#-----------------
|
||||
dfs_combine_wf = [baseline_BT, smnc_BT, ros_BT, rus_BT, rouC_BT,
|
||||
baseline_CV, smnc_CV, ros_CV, rus_CV, rouC_CV]
|
||||
|
||||
dfs_nrows_wf = []
|
||||
for df in dfs_combine_wf:
|
||||
dfs_nrows_wf = dfs_nrows_wf + [len(df)]
|
||||
dfs_nrows_wf = max(dfs_nrows_wf)
|
||||
paramD = {
|
||||
'baseline_paramD': { 'input_df' : X
|
||||
, 'target' : y
|
||||
, 'var_type' : 'mixed'
|
||||
, 'resampling_type': 'none'}
|
||||
|
||||
, 'smnc_paramD': { 'input_df' : X_smnc
|
||||
, 'target' : y_smnc
|
||||
, 'var_type' : 'mixed'
|
||||
, 'resampling_type' : 'smnc'}
|
||||
|
||||
dfs_ncols_wf = []
|
||||
for df in dfs_combine_wf:
|
||||
dfs_ncols_wf = dfs_ncols_wf + [len(df.columns)]
|
||||
dfs_ncols_wf = max(dfs_ncols_wf)
|
||||
, 'ros_paramD': { 'input_df' : X_ros
|
||||
, 'target' : y_ros
|
||||
, 'var_type' : 'mixed'
|
||||
, 'resampling_type' : 'ros'}
|
||||
|
||||
expected_nrows_wf = len(dfs_combine_wf) * dfs_nrows_wf
|
||||
expected_ncols_wf = dfs_ncols_wf
|
||||
, 'rus_paramD' : { 'input_df' : X_rus
|
||||
, 'target' : y_rus
|
||||
, 'var_type' : 'mixed'
|
||||
, 'resampling_type' : 'rus'}
|
||||
|
||||
common_cols_wf = list(set.intersection(*(set(df.columns) for df in dfs_combine_wf)))
|
||||
, 'rouC_paramD' : { 'input_df' : X_rouC
|
||||
, 'target' : y_rouC
|
||||
, 'var_type' : 'mixed'
|
||||
, 'resampling_type' : 'rouC'}
|
||||
}
|
||||
|
||||
if len(common_cols_wf) == dfs_ncols_wf :
|
||||
combined_baseline_wf = pd.concat([df[common_cols_wf] for df in dfs_combine_wf], ignore_index=False)
|
||||
resampling_methods_wf = combined_baseline_wf[['Resampling']]
|
||||
resampling_methods_wf = resampling_methods_wf.drop_duplicates()
|
||||
print('\nConcatenating dfs with different resampling methods [WF]:', tts_split
|
||||
, '\nNo. of dfs combining:', len(dfs_combine_wf)
|
||||
, '\nThe sampling methods are:'
|
||||
, '\n', resampling_methods_wf)
|
||||
if len(combined_baseline_wf) == expected_nrows_wf and len(combined_baseline_wf.columns) == expected_ncols_wf:
|
||||
print('\nPASS:', len(dfs_combine_wf), 'dfs successfully combined'
|
||||
, '\nnrows in combined_df_wf:', len(combined_baseline_wf)
|
||||
, '\nncols in combined_df_wf:', len(combined_baseline_wf.columns))
|
||||
else:
|
||||
print('\nFAIL: concatenating failed'
|
||||
, '\nExpected nrows:', expected_nrows_wf
|
||||
, '\nGot:', len(combined_baseline_wf)
|
||||
, '\nExpected ncols:', expected_ncols_wf
|
||||
, '\nGot:', len(combined_baseline_wf.columns))
|
||||
sys.exit()
|
||||
else:
|
||||
sys.exit('\nConcatenting dfs not possible [WF],check numbers ')
|
||||
# Initial run to get the dict containing CV, BT and metadata DFs
|
||||
mmD = {}
|
||||
for k, v in paramD.items():
|
||||
# print(mmD[k])
|
||||
scores_7030D = MultModelsCl(**paramD[k]
|
||||
, tts_split_type = tts_split_7030
|
||||
, skf_cv = skf_cv
|
||||
, blind_test_df = X_bts
|
||||
, blind_test_target = y_bts
|
||||
, add_cm = True
|
||||
, add_yn = True
|
||||
, return_formatted_output = True)
|
||||
mmD[k] = scores_7030D
|
||||
|
||||
# Extracting the dfs from within the dict and concatenating to output as one df
|
||||
for k, v in mmD.items():
|
||||
out_wf_7030 = pd.concat(mmD, ignore_index = True)
|
||||
|
||||
# Add index as a column
|
||||
combined_baseline_wf.columns
|
||||
combined_baseline_wf = combined_baseline_wf.reset_index()
|
||||
combined_baseline_wf.rename(columns = {'index': 'Model_name'}, inplace = True)
|
||||
combined_baseline_wf.head()
|
||||
|
||||
# sort df: Resampling, Data_source, and MCC
|
||||
combined_baseline_wf.sort_values(by = ['Resampling', 'Data_source', 'MCC'], ascending = [True, True, False], inplace = True)
|
||||
##############################################################################
|
||||
#%% Combine LF
|
||||
#-----------------
|
||||
# Combine LF*
|
||||
#-----------------
|
||||
dfs_combine = [baseline_all, smnc_all, ros_all, rus_all, rouC_all ]
|
||||
|
||||
dfs_nrows = []
|
||||
for df in dfs_combine:
|
||||
dfs_nrows = dfs_nrows + [len(df)]
|
||||
dfs_nrows = max(dfs_nrows)
|
||||
|
||||
dfs_ncols = []
|
||||
for df in dfs_combine:
|
||||
dfs_ncols = dfs_ncols + [len(df.columns)]
|
||||
dfs_ncols = max(dfs_ncols)
|
||||
|
||||
# dfs_ncols = []
|
||||
# dfs_ncols2 = mode(dfs_ncols.append(len(df.columns) for df in dfs_combine)
|
||||
# dfs_ncols2
|
||||
|
||||
expected_nrows = len(dfs_combine) * dfs_nrows
|
||||
expected_ncols = dfs_ncols
|
||||
|
||||
common_cols = list(set.intersection(*(set(df.columns) for df in dfs_combine)))
|
||||
|
||||
if len(common_cols) == dfs_ncols :
|
||||
combined_baseline = pd.concat([df[common_cols] for df in dfs_combine], ignore_index=True)
|
||||
resampling_methods = combined_baseline[['Resampling', 'training_size']]
|
||||
resampling_methods = resampling_methods.drop_duplicates()
|
||||
print('\nConcatenating dfs with different resampling methods:', tts_split
|
||||
, '\nNo. of dfs combining:', len(dfs_combine)
|
||||
, '\nThe sampling methods are:'
|
||||
, '\n', resampling_methods)
|
||||
if len(combined_baseline) == expected_nrows and len(combined_baseline.columns) == expected_ncols:
|
||||
print('\nPASS:', len(dfs_combine), 'dfs successfully combined'
|
||||
, '\nnrows in combined_df:', len(combined_baseline)
|
||||
, '\nncols in combined_df:', len(combined_baseline.columns))
|
||||
else:
|
||||
print('\nFAIL: concatenating failed'
|
||||
, '\nExpected nrows:', expected_nrows
|
||||
, '\nGot:', len(combined_baseline)
|
||||
, '\nExpected ncols:', expected_ncols
|
||||
, '\nGot:', len(combined_baseline.columns))
|
||||
sys.exit()
|
||||
else:
|
||||
sys.exit('\nConcatenting dfs not possible,check numbers ')
|
||||
|
||||
# Add further column indications
|
||||
combined_baseline['test_size'] = bts_size
|
||||
combined_baseline['tts_split'] = tts_split
|
||||
combined_baseline['testY_ratio'] = round(yc2_ratio,2)
|
||||
#combined_baseline.columns
|
||||
|
||||
# change to column names to be lower case for consistency
|
||||
combined_baseline.rename(columns = {'Resampling' : 'resampling'
|
||||
, 'Data_source': 'data_source'}, inplace = True)
|
||||
combined_baseline.columns
|
||||
|
||||
# sort df: resampling, data_source, mcc
|
||||
combined_baseline.sort_values(by = ['resampling', 'data_source', 'score_order'], ascending = [True, True, True], inplace = True)
|
||||
|
||||
# # rpow bind
|
||||
# if all(XXX):
|
||||
# print('\nPASS:colnames match, proceeding to rowbind')
|
||||
# comb_df = pd.concat()], axis = 0, ignore_index = True ) combined_baseline
|
||||
print('\n######################################################################'
|
||||
, '\nEnd--> Successfully generated output DF for Multiple classifiers (baseline models)'
|
||||
, '\nGene:', gene.lower()
|
||||
, '\nDrug:', drug
|
||||
, '\noutput file:', outFile_wf
|
||||
, '\nDim of output:', out_wf_7030.shape
|
||||
, '\n######################################################################')
|
||||
###############################################################################
|
||||
#====================
|
||||
# Write output file
|
||||
#====================
|
||||
combined_baseline_wf.to_csv(outFile_wf, index = False)
|
||||
#out_wf_7030.to_csv(outFile_wf, index = False)
|
||||
print('\nFile successfully written:', outFile_wf)
|
||||
|
||||
combined_baseline.to_csv(outFile_lf, index = False)
|
||||
print('\nFile successfully written:', outFile_lf)
|
||||
###############################################################################
|
||||
Loading…
Add table
Add a link
Reference in a new issue