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msa

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This commit is contained in:
Tanushree Tunstall 2022-09-05 17:03:18 +01:00
parent d5975402bf
commit 7c3c5093c7
1 changed files with 12 additions and 10 deletions
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22
msa/global.R
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@ -31,15 +31,17 @@ library(hash)
# than previous approaches # than previous approaches
# system.time({ # system.time({
# if(interactive()){ if(interactive()){
# source("~/git/LSHTM_analysis/scripts/Header_TT.R") load_dir="~/git/"
# } else {
source("/srv/shiny-server/git/LSHTM_analysis/scripts/Header_TT.R") } else {
# } load_dir="/srv/shiny-server/git/"
}
source(paste0(load_dir,"LSHTM_analysis/scripts/Header_TT.R"))
load_target_globals=function(target){ load_target_globals=function(target){
cat(paste0("Reloading Target: ", target)) cat(paste0("Reloading Target: ", target))
source(paste0("~/git/LSHTM_analysis/config/", target, ".R")) # load per-target config file source(paste0(load_dir, "LSHTM_analysis/config/", target, ".R")) # load per-target config file
invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv)) invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv))
invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv)) invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv))
@ -60,12 +62,12 @@ load_target_globals=function(target){
"mcsm_ppi2"#, "mcsm_ppi2"#,
#"mcsm_na" #"mcsm_na"
), function(x){ ), function(x){
wf_filename=paste0("~/git/Misc/shiny_dashboard/data/", tolower(gene), "-wf_", x ,".csv") wf_filename=paste0(load_dir, "Misc/shiny_dashboard/data/", tolower(gene), "-wf_", x ,".csv")
wf_var=paste0("wf_",x) wf_var=paste0("wf_",x)
if (file.exists(wf_filename)){ if (file.exists(wf_filename)){
invisible(assign(wf_var,read.csv(wf_filename), envir = .GlobalEnv)) # FILTH invisible(assign(wf_var,read.csv(wf_filename), envir = .GlobalEnv)) # FILTH
} }
lf_filename=paste0("~/git/Misc/shiny_dashboard/data/", tolower(gene), "-lf_", x ,".csv") lf_filename=paste0(load_dir, "Misc/shiny_dashboard/data/", tolower(gene), "-lf_", x ,".csv")
lf_var=paste0(target, "_lf_",x) lf_var=paste0(target, "_lf_",x)
if (file.exists(lf_filename)){ if (file.exists(lf_filename)){
invisible(assign(lf_var,read.csv(lf_filename), envir = .GlobalEnv)) # FILTH invisible(assign(lf_var,read.csv(lf_filename), envir = .GlobalEnv)) # FILTH
@ -77,12 +79,12 @@ load_target_globals=function(target){
load_msa_global=function(gene){ load_msa_global=function(gene){
drug=target_map[[gene]] drug=target_map[[gene]]
in_filename_msa = paste0(tolower(gene), "_msa.csv") in_filename_msa = paste0(tolower(gene), "_msa.csv")
infile_msa = paste0("~/git/Data/", drug, "/output/", in_filename_msa) infile_msa = paste0(load_dir,"Data/", drug, "/output/", in_filename_msa)
print(infile_msa) print(infile_msa)
msa1 = read.csv(infile_msa, header = F) msa1 = read.csv(infile_msa, header = F)
msa_seq = msa1$V1 msa_seq = msa1$V1
infile_fasta = paste0("~/git/Data/", drug, "/input/", tolower(gene), "2_f2.fasta") infile_fasta = paste0(load_dir,"Data/", drug, "/input/", tolower(gene), "2_f2.fasta")
print(infile_fasta) print(infile_fasta)
msa2 = read.csv(infile_fasta, header = F) msa2 = read.csv(infile_fasta, header = F)
wt_seq = msa2$V1 wt_seq = msa2$V1