adde script to run ml baseline models orig version with feature groups
This commit is contained in:
parent
137f19a285
commit
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2 changed files with 562 additions and 4 deletions
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@ -419,7 +419,7 @@ def setvars(gene,drug):
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#---------------------------------------
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#---------------------------------------
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#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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#%% Data for ML ###############################################################
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#%% Data for ML
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#==========================
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#==========================
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# Data for ML
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# Data for ML
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#==========================
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#==========================
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@ -428,7 +428,7 @@ def setvars(gene,drug):
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# Build column names to mask for affinity chanhes
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# Build column names to mask for affinity chanhes
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if gene.lower() in geneL_basic:
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if gene.lower() in geneL_basic:
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#X_stabilityN = common_cols_stabiltyN
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#X_stabilityN = common_cols_stabiltyN
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gene_affinity_colnames = []# not needed as its a common one
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gene_affinity_colnames = []# not needed as its the common ones
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cols_to_mask = ['ligand_affinity_change']
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cols_to_mask = ['ligand_affinity_change']
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if gene.lower() in geneL_ppi2:
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if gene.lower() in geneL_ppi2:
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@ -487,7 +487,6 @@ def setvars(gene,drug):
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, 'ddg_foldx'
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, 'ddg_foldx'
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, 'deepddg'
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, 'deepddg'
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, 'ddg_dynamut2'
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, 'ddg_dynamut2'
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, 'mmcsm_lig'
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, 'contacts']
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, 'contacts']
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#--------
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#--------
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# FoldX
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# FoldX
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@ -506,7 +505,8 @@ def setvars(gene,drug):
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# FG3: Affinity features
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# FG3: Affinity features
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#===================
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#===================
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common_affinity_Fnum = ['ligand_distance'
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common_affinity_Fnum = ['ligand_distance'
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, 'ligand_affinity_change']
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, 'ligand_affinity_change'
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, 'mmcsm_lig']
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# if gene.lower() in geneL_basic:
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# if gene.lower() in geneL_basic:
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# X_affinityFN = common_affinity_Fnum
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# X_affinityFN = common_affinity_Fnum
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558
scripts/ml/run_fg.py
Executable file
558
scripts/ml/run_fg.py
Executable file
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@ -0,0 +1,558 @@
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Sat May 28 05:25:30 2022
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@author: tanu
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"""
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import os
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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 = '')
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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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###############################################################################
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homedir = os.path.expanduser("~")
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os.chdir( homedir + '/git/LSHTM_analysis/scripts/ml/')
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#==================
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# Import data
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#==================
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from ml_data_dissected import *
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setvars(gene,drug)
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from ml_data_dissected 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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# TT run all ML clfs: baseline model
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from MultModelsCl import MultModelsCl
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############################################################################
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print('\n#####################################################################\n'
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, '\nRunning ML analysis: feature groups '
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, '\nGene name:', gene
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, '\nDrug name:', drug)
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###############################################################################
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#==================
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# Specify outdir
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#==================
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outdir_ml = outdir + 'ml/uq_v1/fgs/'
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print('\nOutput directory:', outdir_ml)
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outFile = outdir_ml + gene.lower() + '_baseline_FG.csv'
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#==================
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# other vars
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#==================
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tts_split_name = 'original'
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resampling = 'none'
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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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#%%###########################################################################
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print('\n================================================================\n')
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#all_featuresN = X_evolFN + X_structural_FN + X_genomicFN
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# X_structural_FN = X_stability_FN + X_affinityFN + X_resprop_FN
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# X_resprop_FN = X_aaindex_Fnum + X_str_Fnum + X_aap_Fcat
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print('\n================================================================'
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, '\nTotal Evolutionary features (n):' , len(X_evolFN)
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, '\n--------------Evol. feature colnames:', X_evolFN
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, '\n================================================================'
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, '\n\nTotal structural features (n):', len(X_structural_FN)
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, '\n--------Stability ncols:' , len(X_stability_FN)
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, '\n--------------Common stability colnames:' , X_common_stability_Fnum
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, '\n--------------Foldx colnames:' , X_foldX_Fnum
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, '\n--------Affinity ncols:' , len(X_affinityFN)
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, '\n--------------Common affinity colnames:' , common_affinity_Fnum
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, '\n--------------Gene specific affinity colnames:', gene_affinity_colnames
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, '\n--------Residue prop ncols:' , len(X_resprop_FN)
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, '\n--------------Residue Prop cols:' , X_str_Fnum
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, '\n--------------AA change Prop cols:' , X_aap_Fcat
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, '\n--------------AA index cols:' , X_aaindex_Fnum
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, '\n================================================================'
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, '\n\nTotal Genomic features (n):' , len(X_genomicFN)
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, '\n--------MAF+OR cols:' , len(X_gn_mafor_Fnum)
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, '\n--------------MAF+OR colnames:' , X_gn_mafor_Fnum
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, '\n--------Lineage cols:' , len(X_gn_linegae_Fnum)
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, '\n--------------Lineage cols:' , X_gn_linegae_Fnum
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, '\n--------Other cols:' , len(X_gn_Fcat)
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, '\n--------------Other cols:' , X_gn_Fcat
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, '\n================================================================')
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# Sanity check
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if ( len(X.columns) == len(X_evolFN) + len(X_structural_FN) + len(X_genomicFN)):
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print('\nPass: No. of features match')
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else:
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print('\nFail: Count of feature mismatch'
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, '\nExpected:', len(X_evolFN) + len(X_structural_FN) + len(X_genomicFN)
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, '\nGot:', len(X.columns))
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sys.exit()
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print('\n#####################################################################\n')
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###############################################################################
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#================
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# Evolutionary
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# X_evolFN
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#================
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feature_gp_nameEV = 'evolutionary'
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n_featuresEV = len(X_evolFN)
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scores_mmEV = MultModelsCl(input_df = X[X_evolFN]
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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_input_df = X_bts[X_evolFN]
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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_allEV = pd.DataFrame(scores_mmEV)
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baseline_EV = baseline_allEV.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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baseline_EV = baseline_EV.reset_index()
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baseline_EV.rename(columns = {'index': 'original_names'}, inplace = True)
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# Indicate whether BT or CT
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bt_pattern = re.compile(r'bts_.*')
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baseline_EV['data_source'] = baseline_EV.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
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baseline_EV['score_type'] = baseline_EV['original_names'].str.replace('bts_|test_', '', regex = True)
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score_type_uniqueN = set(baseline_EV['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_EV['score_order'] = baseline_EV['score_type'].map(score_type_ordermapD)
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baseline_EV.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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baseline_EV['feature_group'] = feature_gp_nameEV
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baseline_EV['resampling'] = resampling
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baseline_EV['tts_split'] = tts_split_name
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baseline_EV['n_features'] = n_featuresEV
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###############################################################################
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#================
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# Genomics
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# X_genomicFN
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#================
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feature_gp_nameGN = 'genomics'
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n_featuresGN = len(X_genomicFN)
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scores_mmGN = MultModelsCl(input_df = X[X_genomicFN]
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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_input_df = X_bts[X_genomicFN]
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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_allGN = pd.DataFrame(scores_mmGN)
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baseline_GN = baseline_allGN.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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baseline_GN = baseline_GN.reset_index()
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baseline_GN.rename(columns = {'index': 'original_names'}, inplace = True)
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# Indicate whether BT or CT
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bt_pattern = re.compile(r'bts_.*')
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baseline_GN['data_source'] = baseline_GN.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
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baseline_GN['score_type'] = baseline_GN['original_names'].str.replace('bts_|test_', '', regex = True)
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score_type_uniqueN = set(baseline_GN['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_GN['score_order'] = baseline_GN['score_type'].map(score_type_ordermapD)
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baseline_GN.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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baseline_GN['feature_group'] = feature_gp_nameGN
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baseline_GN['resampling'] = resampling
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baseline_GN['tts_split'] = tts_split_name
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baseline_GN['n_features'] = n_featuresGN
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###############################################################################
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#all_featuresN = X_evolFN + X_structural_FN + X_genomicFN
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# X_structural_FN = X_stability_FN + X_affinityFN + X_resprop_FN
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# X_resprop_FN = X_aaindex_Fnum + X_str_Fnum + X_aap_Fcat
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#================
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# Structural cols
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# X_structural_FN
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#================
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feature_gp_nameSTR = 'structural'
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n_featuresSTR = len(X_structural_FN)
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scores_mmSTR = MultModelsCl(input_df = X[X_structural_FN]
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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_input_df = X_bts[X_structural_FN]
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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_allSTR = pd.DataFrame(scores_mmSTR)
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baseline_STR = baseline_allSTR.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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baseline_STR = baseline_STR.reset_index()
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baseline_STR.rename(columns = {'index': 'original_names'}, inplace = True)
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# Indicate whether BT or CT
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bt_pattern = re.compile(r'bts_.*')
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baseline_STR['data_source'] = baseline_STR.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
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baseline_STR['score_type'] = baseline_STR['original_names'].str.replace('bts_|test_', '', regex = True)
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score_type_uniqueN = set(baseline_STR['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_STR['score_order'] = baseline_STR['score_type'].map(score_type_ordermapD)
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baseline_STR.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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baseline_STR['feature_group'] = feature_gp_nameSTR
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baseline_STR['resampling'] = resampling
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baseline_STR['tts_split'] = tts_split_name
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baseline_STR['n_features'] = n_featuresSTR
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##############################################################################
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#================
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# Stability cols
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# X_stability_FN
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#================
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feature_gp_nameSTB = 'stability'
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n_featuresSTB = len(X_stability_FN)
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scores_mmSTB = MultModelsCl(input_df = X[X_stability_FN]
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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_input_df = X_bts[X_stability_FN]
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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_allSTB = pd.DataFrame(scores_mmSTB)
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baseline_STB = baseline_allSTB.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
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baseline_STB = baseline_STB.reset_index()
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baseline_STB.rename(columns = {'index': 'original_names'}, inplace = True)
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# Indicate whether BT or CT
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bt_pattern = re.compile(r'bts_.*')
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baseline_STB['data_source'] = baseline_STB.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
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baseline_STB['score_type'] = baseline_STB['original_names'].str.replace('bts_|test_', '', regex = True)
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score_type_uniqueN = set(baseline_STB['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):
|
||||||
|
print('\nPASS: sorting df by score that is mapped onto the order I want')
|
||||||
|
baseline_STB['score_order'] = baseline_STB['score_type'].map(score_type_ordermapD)
|
||||||
|
baseline_STB.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')
|
||||||
|
|
||||||
|
baseline_STB['feature_group'] = feature_gp_nameSTB
|
||||||
|
baseline_STB['resampling'] = resampling
|
||||||
|
baseline_STB['tts_split'] = tts_split_name
|
||||||
|
baseline_STB['n_features'] = n_featuresSTB
|
||||||
|
###############################################################################
|
||||||
|
#================
|
||||||
|
# Affinity cols
|
||||||
|
# X_affinityFN
|
||||||
|
#================
|
||||||
|
feature_gp_nameAFF = 'affinity'
|
||||||
|
n_featuresAFF = len(X_affinityFN)
|
||||||
|
|
||||||
|
scores_mmAFF = MultModelsCl(input_df = X[X_affinityFN]
|
||||||
|
, target = y
|
||||||
|
, var_type = 'mixed'
|
||||||
|
, skf_cv = skf_cv
|
||||||
|
, blind_test_input_df = X_bts[X_affinityFN]
|
||||||
|
, blind_test_target = y_bts
|
||||||
|
, add_cm = True
|
||||||
|
, add_yn = True)
|
||||||
|
|
||||||
|
baseline_allAFF = pd.DataFrame(scores_mmAFF)
|
||||||
|
|
||||||
|
baseline_AFF = baseline_allAFF.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||||
|
baseline_AFF = baseline_AFF.reset_index()
|
||||||
|
baseline_AFF.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||||
|
|
||||||
|
# Indicate whether BT or CT
|
||||||
|
bt_pattern = re.compile(r'bts_.*')
|
||||||
|
baseline_AFF['data_source'] = baseline_AFF.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||||
|
|
||||||
|
baseline_AFF['score_type'] = baseline_AFF['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||||
|
|
||||||
|
score_type_uniqueN = set(baseline_AFF['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')
|
||||||
|
baseline_AFF['score_order'] = baseline_AFF['score_type'].map(score_type_ordermapD)
|
||||||
|
baseline_AFF.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')
|
||||||
|
|
||||||
|
baseline_AFF['feature_group'] = feature_gp_nameAFF
|
||||||
|
baseline_AFF['resampling'] = resampling
|
||||||
|
baseline_AFF['tts_split'] = tts_split_name
|
||||||
|
baseline_AFF['n_features'] = n_featuresAFF
|
||||||
|
###############################################################################
|
||||||
|
#================
|
||||||
|
# Residue level
|
||||||
|
# X_resprop_FN
|
||||||
|
#================
|
||||||
|
feature_gp_nameRES = 'residue_prop'
|
||||||
|
n_featuresRES = len(X_resprop_FN)
|
||||||
|
|
||||||
|
scores_mmRES = MultModelsCl(input_df = X[X_resprop_FN]
|
||||||
|
, target = y
|
||||||
|
, var_type = 'mixed'
|
||||||
|
, skf_cv = skf_cv
|
||||||
|
, blind_test_input_df = X_bts[X_resprop_FN]
|
||||||
|
, blind_test_target = y_bts
|
||||||
|
, add_cm = True
|
||||||
|
, add_yn = True)
|
||||||
|
|
||||||
|
baseline_allRES = pd.DataFrame(scores_mmRES)
|
||||||
|
|
||||||
|
baseline_RES = baseline_allRES.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||||
|
baseline_RES = baseline_RES.reset_index()
|
||||||
|
baseline_RES.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||||
|
|
||||||
|
# Indicate whether BT or CT
|
||||||
|
bt_pattern = re.compile(r'bts_.*')
|
||||||
|
baseline_RES['data_source'] = baseline_RES.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||||
|
|
||||||
|
baseline_RES['score_type'] = baseline_RES['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||||
|
|
||||||
|
score_type_uniqueN = set(baseline_RES['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')
|
||||||
|
baseline_RES['score_order'] = baseline_RES['score_type'].map(score_type_ordermapD)
|
||||||
|
baseline_RES.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')
|
||||||
|
|
||||||
|
baseline_RES['feature_group'] = feature_gp_nameRES
|
||||||
|
baseline_RES['resampling'] = resampling
|
||||||
|
baseline_RES['tts_split'] = tts_split_name
|
||||||
|
baseline_RES['n_features'] = n_featuresRES
|
||||||
|
###############################################################################
|
||||||
|
#================
|
||||||
|
# Residue level-AAindex
|
||||||
|
#X_resprop_FN - X_aaindex_Fnum
|
||||||
|
#================
|
||||||
|
X_respropNOaaFN = list(set(X_resprop_FN) - set(X_aaindex_Fnum))
|
||||||
|
|
||||||
|
feature_gp_nameRNAA = 'ResPropNoAA'
|
||||||
|
n_featuresRNAA = len(X_respropNOaaFN)
|
||||||
|
|
||||||
|
scores_mmRNAA = MultModelsCl(input_df = X[X_respropNOaaFN]
|
||||||
|
, target = y
|
||||||
|
, var_type = 'mixed'
|
||||||
|
, skf_cv = skf_cv
|
||||||
|
, blind_test_input_df = X_bts[X_respropNOaaFN]
|
||||||
|
, blind_test_target = y_bts
|
||||||
|
, add_cm = True
|
||||||
|
, add_yn = True)
|
||||||
|
|
||||||
|
baseline_allRNAA = pd.DataFrame(scores_mmRNAA)
|
||||||
|
|
||||||
|
baseline_RNAA = baseline_allRNAA.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||||
|
baseline_RNAA = baseline_RNAA.reset_index()
|
||||||
|
baseline_RNAA.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||||
|
|
||||||
|
# Indicate whether BT or CT
|
||||||
|
bt_pattern = re.compile(r'bts_.*')
|
||||||
|
baseline_RNAA['data_source'] = baseline_RNAA.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||||
|
|
||||||
|
baseline_RNAA['score_type'] = baseline_RNAA['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||||
|
|
||||||
|
score_type_uniqueN = set(baseline_RNAA['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')
|
||||||
|
baseline_RNAA['score_order'] = baseline_RNAA['score_type'].map(score_type_ordermapD)
|
||||||
|
baseline_RNAA.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')
|
||||||
|
|
||||||
|
baseline_RNAA['feature_group'] = feature_gp_nameRNAA
|
||||||
|
baseline_RNAA['resampling'] = resampling
|
||||||
|
baseline_RNAA['tts_split'] = tts_split_name
|
||||||
|
baseline_RNAA['n_features'] = n_featuresRNAA
|
||||||
|
###############################################################################
|
||||||
|
#================
|
||||||
|
# Structural cols-AAindex
|
||||||
|
#X_structural_FN - X_aaindex_Fnum
|
||||||
|
#================
|
||||||
|
X_strNOaaFN = list(set(X_structural_FN) - set(X_aaindex_Fnum))
|
||||||
|
|
||||||
|
feature_gp_nameSNAA = 'StrNoAA'
|
||||||
|
n_featuresSNAA = len(X_strNOaaFN)
|
||||||
|
|
||||||
|
scores_mmSNAA = MultModelsCl(input_df = X[X_strNOaaFN]
|
||||||
|
, target = y
|
||||||
|
, var_type = 'mixed'
|
||||||
|
, skf_cv = skf_cv
|
||||||
|
, blind_test_input_df = X_bts[X_strNOaaFN]
|
||||||
|
, blind_test_target = y_bts
|
||||||
|
, add_cm = True
|
||||||
|
, add_yn = True)
|
||||||
|
|
||||||
|
baseline_allSNAA = pd.DataFrame(scores_mmSNAA)
|
||||||
|
|
||||||
|
baseline_SNAA = baseline_allSNAA.filter(regex = 'bts_.*|test_.*|.*_time|TN|FP|FN|TP|.*_neg|.*_pos', axis = 0)
|
||||||
|
baseline_SNAA = baseline_SNAA.reset_index()
|
||||||
|
baseline_SNAA.rename(columns = {'index': 'original_names'}, inplace = True)
|
||||||
|
|
||||||
|
# Indicate whether BT or CT
|
||||||
|
bt_pattern = re.compile(r'bts_.*')
|
||||||
|
baseline_SNAA['data_source'] = baseline_SNAA.apply(lambda row: 'BT' if bt_pattern.search(row.original_names) else 'CV' , axis = 1)
|
||||||
|
|
||||||
|
baseline_SNAA['score_type'] = baseline_SNAA['original_names'].str.replace('bts_|test_', '', regex = True)
|
||||||
|
|
||||||
|
score_type_uniqueN = set(baseline_SNAA['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')
|
||||||
|
baseline_SNAA['score_order'] = baseline_SNAA['score_type'].map(score_type_ordermapD)
|
||||||
|
baseline_SNAA.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')
|
||||||
|
|
||||||
|
baseline_SNAA['feature_group'] = feature_gp_nameSNAA
|
||||||
|
baseline_SNAA['resampling'] = resampling
|
||||||
|
baseline_SNAA['tts_split'] = tts_split_name
|
||||||
|
baseline_SNAA['n_features'] = n_featuresSNAA
|
||||||
|
###############################################################################
|
||||||
|
#%% COMBINING all FG dfs
|
||||||
|
#================
|
||||||
|
# Combine all
|
||||||
|
# https://stackoverflow.com/questions/39862654/pandas-concat-of-multiple-data-frames-using-only-common-columns
|
||||||
|
#================
|
||||||
|
dfs_combine = [baseline_EV, baseline_GN, baseline_STR, baseline_STB, baseline_AFF, baseline_RES , baseline_RNAA , baseline_SNAA]
|
||||||
|
|
||||||
|
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_FG_baseline = pd.concat([df[common_cols] for df in dfs_combine], ignore_index=True)
|
||||||
|
fgs = combined_FG_baseline[['feature_group', 'n_features']]
|
||||||
|
fgs = fgs.drop_duplicates()
|
||||||
|
print('\nConcatenating dfs with feature groups after ML analysis (sampling type):'
|
||||||
|
, '\nNo. of dfs combining:', len(dfs_combine)
|
||||||
|
, '\nSampling type:', resampling
|
||||||
|
, '\nThe feature groups are:'
|
||||||
|
, '\n', fgs)
|
||||||
|
if len(combined_FG_baseline) == expected_nrows and len(combined_FG_baseline.columns) == expected_ncols:
|
||||||
|
print('\nPASS:', len(dfs_combine), 'dfs successfully combined'
|
||||||
|
, '\nnrows in combined_df:', len(combined_FG_baseline)
|
||||||
|
, '\nncols in combined_df:', len(combined_FG_baseline.columns))
|
||||||
|
else:
|
||||||
|
print('\nFAIL: concatenating failed'
|
||||||
|
, '\nExpected nrows:', expected_nrows
|
||||||
|
, '\nGot:', len(combined_FG_baseline)
|
||||||
|
, '\nExpected ncols:', expected_ncols
|
||||||
|
, '\nGot:', len(combined_FG_baseline.columns))
|
||||||
|
sys.exit()
|
||||||
|
else:
|
||||||
|
sys.exit('\nConcatenting dfs not possible,check numbers ')
|
||||||
|
|
||||||
|
# # rpow bind
|
||||||
|
# if all(ll((baseline_EV.columns == baseline_GN.columns == baseline_STR.columns)):
|
||||||
|
# print('\nPASS:colnames match, proceeding to rowbind')
|
||||||
|
# comb_df = pd.concat()], axis = 0, ignore_index = True )
|
||||||
|
###############################################################################
|
||||||
|
#====================
|
||||||
|
# Write output file
|
||||||
|
#====================
|
||||||
|
|
||||||
|
combined_FG_baseline.to_csv(outFile, index = False)
|
||||||
|
print('\nFile successfully written:', outFile)
|
||||||
|
###############################################################################
|
||||||
Loading…
Add table
Add a link
Reference in a new issue