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output merged_df3 and merged_df2 files for all gene-targtes along with active site residues annotated

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Tanushree Tunstall 2022-03-04 10:58:14 +00:00
parent bff16fc219
commit 51069fdb76
1 changed files with 25 additions and 44 deletions
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69
ml_data/ml_data.R
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@ -5,61 +5,42 @@
# pyrazinamide: 0 and 1, loss of data # pyrazinamide: 0 and 1, loss of data
# mutation_info_labels: DM and OM, full data # mutation_info_labels: DM and OM, full data
################################################## ##################################################
# ONLY ONCE
#source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#write.csv(colnames(merged_df3), "data_colnames.csv")
#---------------------------------------------------
colnames_order_pnca = read.csv("~/git/ML_AI_training/ml_data/colnames_order.csv"
, header = F)
# reorder columns by name
colnames_order_pnca <- colnames_order_pnca$V1
################################################### ###################################################
#config_gene = c("alr", "embb", "gid", "katg", "pnca", "rpob") #config_gene = c("alr", "embb", "gid", "katg", "pnca", "rpob")
#config_gene = c("alr", "embb") #config_gene = c("alr", "embb")
#sapply(config_gene, function(x) source(paste0("~/git/LSHTM_analysis/config/", x, ".R")), USE.NAMES = F) #sapply(config_gene, function(x) source(paste0("~/git/LSHTM_analysis/config/", x, ".R")), USE.NAMES = F)
#----------------------------------------------------
#source("~/git/LSHTM_analysis/config/alr.R") #source("~/git/LSHTM_analysis/config/alr.R")
# FIXME: "cycloserine" "mcsm_ppi2_affinity" "mcsm_ppi2_scaled" "mcsm_ppi2_outcome" "interface_dist" #source("~/git/LSHTM_analysis/config/embb.R")
# source("~/git/LSHTM_analysis/config/embb.R") #source("~/git/LSHTM_analysis/config/gid.R")
# source("~/git/LSHTM_analysis/config/gid.R") #source("~/git/LSHTM_analysis/config/katg.R")
# source("~/git/LSHTM_analysis/config/katg.R") #source("~/git/LSHTM_analysis/config/pnca.R")
source("~/git/LSHTM_analysis/config/pnca.R") source("~/git/LSHTM_analysis/config/rpob.R")
# source("~/git/LSHTM_analysis/config/rpob.R") #----------------------------------------------------
##################################################
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
###################################################### ######################################################
gene; drug
merged_df3$active_aa_pos = ifelse(merged_df3$position %in% active_aa_pos , 1, 0)
table(merged_df3$active_aa_pos)
mdf3_outName = paste0(outdir, "/", tolower(gene), "_merged_df3.csv") mdf3_outName = paste0(outdir, "/", tolower(gene), "_merged_df3.csv")
mdf3_outName mdf3_outName
if( (length(colnames_order) == ncol(merged_df3)) && (all(colnames_order %in%colnames(merged_df3))) ){ cat("\nWriting output file:", mdf3_outName)
cat("\nProceeding with rearranging columns in merged_df3") write.csv(merged_df3, mdf3_outName, row.names = F)
merged_df3_o = merged_df3[ , colnames_order] cat("\nnrows:" , nrow(merged_df3)
cat("\nWriting output file:", mdf3_outName) , "\nncols:" , ncol(merged_df3))
write.csv(merged_df3_o, mdf3_outName, row.names = F)
cat("\nnrows:" , nrow(merged_df3_o) #=========================================================
, "\nncols:" , ncol(merged_df3_o)) merged_df2$active_aa_pos = ifelse(merged_df2$position %in% active_aa_pos , 1, 0)
table(merged_df2$active_aa_pos)
}else
cat("length mismatch:"
, colnames(merged_df3)[!colnames(merged_df3)%in%(colnames_order )]
)
mdf2_outName = paste0(outdir, "/", tolower(gene), "_merged_df2.csv") mdf2_outName = paste0(outdir, "/", tolower(gene), "_merged_df2.csv")
mdf2_outName mdf2_outName
if( (length(colnames_order) == ncol(merged_df2)) && (all(colnames_order %in%colnames(merged_df2))) ){ cat("\nWriting output file:", mdf2_outName)
cat("\nProceeding with rearranging columns in merged_df3") write.csv(merged_df2, mdf2_outName, row.names = F)
merged_df2_o = merged_df2[ , colnames_order] cat("\nnrows:" , nrow(merged_df2)
cat("\nWriting output file:", mdf2_outName) , "\nncols:" , ncol(merged_df2))
write.csv(merged_df2_o, mdf2_outName, row.names = F)
cat("\nnrows:" , nrow(merged_df2_o)
, "\nncols:" , ncol(merged_df2_o))
}