script to subset data for dnds cals

scripts/data_selective_pressure.R

@@ -0,0 +1,70 @@
+#!/usr/bin/env Rscript
+#########################################################
+# TASK: Data for selective pressure (dnds calcs)
+
+# Output:2 csv
+#=======================================================================
+# working dir and loading libraries
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/")
+getwd()
+
+source("plotting/combining_dfs_plotting.R")
+
+#=========================
+#=======
+# output
+#=======
+select_pressure_muts_all = paste0(outdir,"/", tolower(gene), "_dnds_all_muts.csv")
+
+select_pressure_muts_aa_site = paste0(outdir,"/", tolower(gene), "_dnds_active_site_muts.csv")
+#=======================================================================
+#----------
+# df1
+#----------
+colnames(merged_df2)
+cols_to_select = c("id", "sample"
+                   , "mutation"
+                   , "mutationinformation"
+                   , "wild_type"
+                   , "position"
+                   , "mutant_type")
+
+dnds_df_all = merged_df2[, cols_to_select]
+
+#-----------------------
+# df2: active site only
+#-----------------------
+str(dnds_df_all)
+is.numeric(dnds_df_all$position)
+
+active_site_positions = c(8, 13, 49, 51, 57, 68, 71, 96, 103, 133, 134, 137, 138)
+
+aa_site_i = which(dnds_df_all$position%in%active_site_positions)
+dnds_df_aa_site = dnds_df_all[dnds_df_all$position%in%active_site_positions,]
+
+if (all(rownames(dnds_df_aa_site) == aa_site_i) ){
+  cat("PASS: active site positions subsetted correctly")
+}else{
+  cat("FAIL: active site positions mismatch")
+  quit()
+}
+
+table(dnds_df_aa_site$position)
+
+#=======================================================================
+#==============
+# write output
+#=============
+
+#----------
+# df1
+#----------
+cat("Filename:", select_pressure_muts_all)
+write.csv(dnds_df_all, select_pressure_muts_all, row.names = FALSE)
+
+#----------
+# df1
+#----------
+cat("Filename:", select_pressure_muts_aa_site)
+write.csv(dnds_df_aa_site, select_pressure_muts_aa_site, row.names = FALSE)