98 lines
3 KiB
Python
98 lines
3 KiB
Python
#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Fri Jun 24 11:07:05 2022
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@author: tanu
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"""
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import re
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import argparse
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###############################################################################
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# gene = 'pncA'
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# drug = 'pyrazinamide'
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#total_mtblineage_uc = 8
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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 = 'pncA')
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arg_parser.add_argument('-g', '--gene', help = 'gene name', default = 'pyrazinamide')
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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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###############################################################################
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###############################################################################
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#==================
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# Import data
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#==================
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from ml_data_7030 import *
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setvars(gene,drug)
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from ml_data_7030 import *
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# from YC run_all_ML: run locally
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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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#====================
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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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#==================
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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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###############################################################################
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print('\n#####################################################################\n'
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, '\nRunning ML analysis: Multiple models'
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, '\nGene name:', gene
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, '\nDrug name:', drug)
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###############################################################################
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#%% Test MultModelsCL WITHOUT returning formatted output
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#================
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# MultModelsCl: without formatted output
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#================
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mmD = MultModelsCl(input_df = X_smnc
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, target = y_smnc
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, var_type = 'mixed'
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, tts_split_type = tts_split_7030
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, resampling_type = 'smnc'
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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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, return_formatted_output = False)
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#================
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# MultModelsCl: WITH formatted output
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#================
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mmDF = MultModelsCl(input_df = X_smnc
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, target = y_smnc
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, var_type = 'mixed'
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, tts_split_type = tts_split_7030
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, resampling_type = 'smnc'
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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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, return_formatted_output= True )
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#=================
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# test function
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#=================
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# output from function call
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ProcessMultModelCl(smnc_scores_mmD)
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