From e5f882841e0fb39f12023508e17f6ca23d26bacd Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sat, 2 Jul 2022 16:57:41 +0100
Subject: [PATCH] added cm_datai.py to get data for cm model for running fs
 later

---
 scripts/ml/combined_model/cm_datai.py | 136 ++++++++++++++++++++++++++
 1 file changed, 136 insertions(+)
 create mode 100644 scripts/ml/combined_model/cm_datai.py

diff --git a/scripts/ml/combined_model/cm_datai.py b/scripts/ml/combined_model/cm_datai.py
new file mode 100644
index 0000000..b41e980
--- /dev/null
+++ b/scripts/ml/combined_model/cm_datai.py
@@ -0,0 +1,136 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Jun 29 19:44:06 2022
+
+@author: tanu
+"""
+import sys, os
+import pandas as pd
+import numpy as np
+import re
+from copy import deepcopy
+from sklearn import linear_model
+from sklearn import datasets
+from collections import Counter
+###############################################################################
+homedir = os.path.expanduser("~")
+sys.path.append(homedir + '/git/LSHTM_analysis/scripts/ml/ml_functions')
+sys.path
+###############################################################################
+outdir = homedir + '/git/LSHTM_ML/output/combined/'
+
+#====================
+# Import ML functions 
+#====================
+from ml_data_combined import *
+from MultClfs_logo_skf import *
+#from GetMLData import *
+#from SplitTTS import *
+
+skf_cv = StratifiedKFold(n_splits = 10 , shuffle = True, random_state = 42)
+
+#logo = LeaveOneGroupOut()
+
+########################################################################
+# COMPLETE data: No tts_split
+########################################################################
+#%%
+def CMLogoData(cm_input_df = pd.DataFrame()
+        , all_genes =  ["embb", "katg", "rpob", "pnca", "gid", "alr"]
+        , bts_genes = ["embb", "katg"
+                       , "rpob", "pnca", "gid"
+                       ]
+        , cols_to_drop = ['dst', 'dst_mode', 'gene_name']
+        , target_var = 'dst_mode'
+        , gene_group = 'gene_name'
+        , std_gene_omit = []
+        ):
+
+    cm_dataD = {}
+    for bts_gene in bts_genes:
+        print('\n BTS gene:', bts_gene)
+        
+        if not std_gene_omit:
+            training_genesL = ['alr']
+        else:
+            training_genesL = []
+            
+        tr_gene_omit = std_gene_omit + [bts_gene]
+        n_tr_genes = (len(bts_genes) - (len(std_gene_omit)))
+        #n_total_genes = (len(bts_genes) - len(std_gene_omit))
+        n_total_genes = len(all_genes)
+        
+        training_genesL = training_genesL + list(set(bts_genes) - set(tr_gene_omit))
+        #training_genesL = [element for element in bts_genes if element not in tr_gene_omit]
+    
+        print('\nTotal genes: ', n_total_genes
+              ,'\nTraining on:', n_tr_genes
+              ,'\nTraining on genes:', training_genesL
+              , '\nOmitted genes:', tr_gene_omit
+              , '\nBlind test gene:', bts_gene) 
+            
+        tts_split_type = "logo_skf_BT_" + bts_gene
+        
+        outFile = outdir + str(n_tr_genes+1) + "genes_" + tts_split_type + ".csv"
+        
+        print(outFile)
+        
+        bts_geneD = {}
+        #-------
+        # training
+        #------
+        cm_training_df = cm_input_df[~cm_input_df['gene_name'].isin(tr_gene_omit)]
+        
+        cm_X = cm_training_df.drop(cols_to_drop, axis=1, inplace=False)
+        #cm_y = cm_training_df.loc[:,'dst_mode']
+        cm_y = cm_training_df.loc[:, target_var]
+    
+        gene_group = cm_training_df.loc[:,'gene_name']
+        
+        print('\nTraining data dim:', cm_X.shape
+              , '\nTraining Target dim:', cm_y.shape)
+        
+        if all(cm_X.columns.isin(cols_to_drop) == False):
+            print('\nChecked training df does NOT have Target var')
+        else:
+            sys.exit('\nFAIL: training data contains Target var')
+        
+        #---------------
+        # BTS: genes
+        #---------------
+        cm_test_df = cm_input_df[cm_input_df['gene_name'].isin([bts_gene])]
+        
+        cm_bts_X = cm_test_df.drop(cols_to_drop, axis = 1, inplace = False)
+        #cm_bts_y = cm_test_df.loc[:, 'dst_mode']
+        cm_bts_y = cm_test_df.loc[:, target_var]
+    
+        print('\nTEST data dim:', cm_bts_X.shape
+              , '\nTEST Target dim:', cm_bts_y.shape)
+        
+        
+        bts_geneD = {'cm_X'      : cm_X
+                     , 'cm_y'    : cm_y
+                     , 'cm_bts_X': cm_bts_X
+                     , 'cm_bts_y': cm_bts_y}
+        
+        cm_dataD[bts_gene] = bts_geneD
+
+    return(cm_dataD)
+
+#%%
+df_complete_6g = CMLogoData(cm_input_df = combined_df, std_gene_omit=[] )
+df_complete_5g = CMLogoData(cm_input_df = combined_df, std_gene_omit=['alr'])
+# checks
+
+len(df_complete_6g['embb']['cm_X'])
+#len(df_complete_6g['embb']['cm_y'])
+
+len(df_complete_5g['embb']['cm_X'])
+#len(df_complete_5g['embb']['cm_y'])
+
+df_actual_6g = CMLogoData(cm_input_df = combined_df_actual, std_gene_omit=[] )
+df_actual_5g = CMLogoData(cm_input_df = combined_df_actual, std_gene_omit=['alr'])
+
+len(df_actual_6g['embb']['cm_X'])
+len(df_actual_5g['embb']['cm_X'])