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changed dir for reading func in pnca_config.py

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Tanushree Tunstall 2022-06-17 16:37:07 +01:00
parent 96d4e61dca
commit e6d3692445
2 changed files with 10 additions and 14 deletions
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18
scripts/ml/ml_data.py
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@ -423,9 +423,9 @@ def setvars(gene,drug):
#==========================
my_df_ml = my_df.copy()
#==========================
# BLIND test set
#==========================
#===============================
# Training and BLIND test set
#===============================
# Separate blind test set
my_df_ml[drug].isna().sum()
@ -435,7 +435,7 @@ def setvars(gene,drug):
training_df = my_df_ml[my_df_ml[drug].notna()]
training_df.shape
# Target1: dst
# Target1: dst_mode
training_df[drug].value_counts()
training_df['dst_mode'].value_counts()
@ -514,11 +514,7 @@ def setvars(gene,drug):
print('\nTotal no. of features for aaindex:', len(X_aaindexFN))
#%% Construct numerical and categorical column names
# numerical feature names
# numerical_FN = common_cols_stabiltyN + foldX_cols + X_strFN + X_evolFN + X_genomicFN
#numerical_FN = X_ssFN + X_evolFN + X_genomicFN
numerical_FN = X_ssFN + X_evolFN + X_genomicFN + X_aaindexFN
@ -534,8 +530,8 @@ def setvars(gene,drug):
, 'electrostatics_change'
, 'polarity_change'
, 'water_change'
#, 'drtype_mode_labels' # beware then you can't use it to predict [USED it for uq_v1]
, 'active_site'
, 'drtype_mode_labels' # beware then you can't use it to predict [USED it for uq_v1, not v2]
, 'active_site' #[didn't use it for uq_v1]
#, 'gene_name' # will be required for the combined stuff
]
#----------------------------------------------
@ -561,7 +557,7 @@ def setvars(gene,drug):
my_df_ml.groupby('mutationinformation')['ligand_distance'].apply(lambda x: (x>10)).value_counts()
my_df_ml.loc[(my_df_ml['ligand_distance'] > 10), cols_to_mask].value_counts()
# mask the column ligand distance > 10
# mask the mcsm affinity related columns where ligand distance > 10
my_df_ml.loc[(my_df_ml['ligand_distance'] > 10), cols_to_mask] = 0
(my_df_ml['ligand_affinity_change'] == 0).sum()

4
scripts/ml/pnca_config.py
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@ -13,7 +13,7 @@ drug = 'pyrazinamide'
#total_mtblineage_uc = 8
homedir = os.path.expanduser("~")
os.chdir( homedir + '/git/ML_AI_training/')
os.chdir( homedir + '/git/LSHTM_analysis/scripts/ml/')
#---------------------------
# Version 1: no AAindex
@ -30,7 +30,7 @@ from ml_data import *
#from UQ_yc_RunAllClfs import run_all_ML
# TT run all ML clfs: baseline mode
from UQ_MultModelsCl import MultModelsCl
from MultModelsCl import MultModelsCl
#%%###########################################################################