added active site indication for merged_dfs in count_vars_ML.R and also added 'gene_name' in combining_dfs.py

scripts/combining_dfs.py

@@ -124,7 +124,7 @@ if gene.lower() == "embb":
     print("\nReading mCSM file for gene:", gene)
     #in_filename_mcsm = gene.lower() + '_complex_mcsm_norm1.csv' #798
     #in_filename_mcsm = gene.lower() + '_complex_mcsm_norm2.csv' #844
-    in_filename_mcsm = gene.lower() + '_complex_mcsm_norm3.csv' #851
+    in_filename_mcsm = gene.lower() + '_complex_mcsm_norm3.csv' #858 [got all muts on 15/05/2022]
 
 if gene.lower() in gene_list_normal:
    print("\nReading mCSM file for gene:", gene)
@@ -1081,21 +1081,35 @@ combined_df = pd.merge(combined_7dfs
 
 combined_df_expected_cols = len(combined_7dfs.columns) + len(snap2_df_f.columns) - len(merging_cols_m4_v2)
    
-#%% Dimension checks for combined_df:
+#%% Dimension checks for combined_df: specially because embB didn't have mCSM 
+# values for all muts. This was fixed in UQ, and this rerun on 15/05/2022
+#------------------------------------------------------------------------------
+# No longer required since mCSM values for fetched for all muts!
 # CHECK whether logic effects anything else!
-if not gene == "embB":
-    print("\nGene is:", gene)
-    if len(combined_df) == len(mcsm_df) and len(combined_df.columns) == combined_df_expected_cols:
-        print('PASS: successfully combined 8 dfs'
-              , '\nNo. of rows combined_df:', len(combined_df)
-              , '\nNo. of cols combined_df:', len(combined_df.columns))   
-elif len(combined_df) == len(foldx_df) and len(combined_df.columns) == combined_df_expected_cols:
+# if not gene == "embB":
+#     print("\nGene is:", gene)
+#     if len(combined_df) == len(mcsm_df) and len(combined_df.columns) == combined_df_expected_cols:
+#         print('PASS: successfully combined 8 dfs'
+#               , '\nNo. of rows combined_df:', len(combined_df)
+#               , '\nNo. of cols combined_df:', len(combined_df.columns))   
+# elif len(combined_df) == len(foldx_df) and len(combined_df.columns) == combined_df_expected_cols:
+#     print('PASS: successfully combined 8 dfs'
+#                , '\nNo. of rows combined_df:', len(combined_df)
+#                , '\nNo. of cols combined_df:', len(combined_df.columns))
+# else:
+#     sys.exit('FAIL: check individual merges for seventh merge')      
+#------------------------------------------------------------------------------
+print("\nRunning Dimension check for combined_df for gene:", gene)
+
+if len(combined_df) == len(mcsm_df) and len(combined_df.columns) == combined_df_expected_cols:
     print('PASS: successfully combined 8 dfs'
-               , '\nNo. of rows combined_df:', len(combined_df)
-               , '\nNo. of cols combined_df:', len(combined_df.columns))
+          , '\nNo. of rows combined_df:', len(combined_df)
+          , '\nNo. of cols combined_df:', len(combined_df.columns))   
 else:
-    sys.exit('FAIL: check individual merges for seventh merge')        
-            
+    sys.exit('FAIL: check individual merges for seventh merge')    
+
+print('\n====================================================')
+
 print('\nResult of Seventh merge:', combined_df.shape
       , '\n===================================================================')
 
@@ -1361,6 +1375,12 @@ else:
           , '\nGot:', len(combined_all_params_f2.columns) 
           , '\nExpected nrows:', expected_nrows
           , '\nGot:', len(combined_all_params_f2) )
+    
+#---------------------------------------
+# Add gene name
+#---------------------------------------
+combined_all_params_f2['gene_name'] = gene.lower()
+    
 #---------------------------------------
 # Add pdb_file name at the end
 #---------------------------------------

scripts/count_vars_ML.R

@@ -2,13 +2,33 @@
 
 #source("~/git/LSHTM_analysis/config/alr.R")
 #source("~/git/LSHTM_analysis/config/embb.R")
-#source("~/git/LSHTM_analysis/config/gid.R")
+##source("~/git/LSHTM_analysis/config/gid.R")
 #source("~/git/LSHTM_analysis/config/katg.R")
 #source("~/git/LSHTM_analysis/config/pnca.R")
-#source("~/git/LSHTM_analysis/config/rpob.R")
+source("~/git/LSHTM_analysis/config/rpob.R")
 
 source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
+################################################
+# Add acticve site indication
+###############################################
+merged_df2$active_site      = as.integer(merged_df2$position %in% active_aa_pos)
+merged_df2_comp$active_site = as.integer(merged_df2_comp$position %in% active_aa_pos)
+
+merged_df3$active_site      = as.integer(merged_df3$position %in% active_aa_pos)
+merged_df3_comp$active_site = as.integer(merged_df3_comp$position %in% active_aa_pos)
+
+# sanity check
+table(merged_df2$active_site)
+table(merged_df3$active_site)
+
+if( all(table(merged_df2$active_site) == table(as.integer(merged_df2$position %in% active_aa_pos))) &&
+    all(table(merged_df3$active_site) == table(as.integer(merged_df3$position %in% active_aa_pos)))
+){
+  cat('\nActive site indications successfully applied to merged_dfs for gene:', tolower(gene))
+}
+
+
 gene
 gene_match
 
@@ -68,6 +88,9 @@ sum(table(merged_df3$drtype_mode_labels))
 table(merged_df3$lineage)
 sum(table(merged_df3$lineage_labels))
 
+cat("\nWriting merged_df3 for:"
+    , "\nDrug:", drug
+    , "\nGene:", gene)
 # write file
 outfile_merged_df3 = paste0(outdir, '/', tolower(gene), '_merged_df3.csv')
 outfile_merged_df3

scripts/plotting/get_plotting_dfs.R

@@ -87,6 +87,7 @@ merged_df2      = all_plot_dfs[[1]]
 merged_df3      = all_plot_dfs[[2]]
 merged_df2_comp = all_plot_dfs[[3]]
 merged_df3_comp = all_plot_dfs[[4]]
+
 #======================================================================
 
 ####################################################################