Changed system to system2

crisprVerse · Jul 24, 2022 · 4af68d2 · 4af68d2
1 parent 1de382d
commit 4af68d2
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Showing 6 changed files with 46 additions and 29 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -36,6 +36,7 @@ importFrom(basilisk,basiliskStop)
 importFrom(basilisk,obtainEnvironmentPath)
 importFrom(basilisk,setBasiliskFork)
 importFrom(basilisk.utils,activateEnvironment)
+importFrom(basilisk.utils,deactivateEnvironment)
 importFrom(methods,is)
 importFrom(randomForest,randomForest)
 importFrom(reticulate,import_from_path)

diff --git a/R/getAzimuthScores.R b/R/getAzimuthScores.R
@@ -67,22 +67,24 @@ getAzimuthScores <- function(sequences, fork=FALSE){
 
       # Ready to get the scores
     env <- basilisk::obtainEnvironmentPath(env_azimuth)
-    basilisk.utils::activateEnvironment(env)
+    envls <- basilisk.utils::activateEnvironment(env)
+    on.exit(basilisk.utils::deactivateEnvironment(envls))
     programFile <- system.file("python",
                                "azimuth/getAzimuth.py",
                                package="crisprScore",
                                mustWork=TRUE)
-    cmd <- paste0("python ",
-                  programFile, " ",
-                  inputfile, " ",
-                  outputfile)
+    #cmd <- paste0("python ",
+    #              programFile, " ",
+    #              inputfile, " ",
+    #              outputfile)
 
     if (sum(good)>0){
         if (sum(good)==1){
             sequences.valid <- rep(sequences.valid, 2)
         }
         .dumpToFile(sequences.valid, inputfile)
-        system(cmd)
+        system2("python",
+                c(programFile, inputfile, outputfile))
         scores <- read.table(outputfile)[,1]
         if (sum(good)==1){
             scores <- scores[1]

diff --git a/R/getDeepCpf1Scores.R b/R/getDeepCpf1Scores.R
@@ -39,9 +39,13 @@
 #' @inheritParams getAzimuthScores
 #' @export 
 #' @importFrom basilisk basiliskStart basiliskStop basiliskRun
+#' @importFrom basilisk.utils activateEnvironment
+#' @importFrom basilisk.utils deactivateEnvironment
 getDeepCpf1Scores <- function(sequences,
                               convertPAM=TRUE,
-                              fork=FALSE){
+                              fork=FALSE
+){
+
     if (.Platform$OS.type=="windows"){
         stop("DeepCpf1 is not available for Windows at the moment.")
     }
@@ -74,18 +78,21 @@ getDeepCpf1Scores <- function(sequences,
 
     # Ready to get the scores
     env <- basilisk::obtainEnvironmentPath(env_deepcpf1)
-    basilisk.utils::activateEnvironment(env)
+    envls <- basilisk.utils::activateEnvironment(env)
+    on.exit(basilisk.utils::deactivateEnvironment(envls))
     programFile <- system.file("python",
                                "deepcpf1/getDeepCpf1.py",
                                package="crisprScore",
                                mustWork=TRUE)
-    cmd <- paste0("python ",
-                  programFile, " ",
-                  inputfile, " ",
-                  outputfile)
+    #cmd <- paste0("python ",
+    #              programFile, " ",
+    #              inputfile, " ",
+    #              outputfile)
     if (sum(good)>0){
         .dumpToFile(sequences.valid, inputfile)
-        system(cmd)
+        #system(cmd)
+        system2("python",
+                c(programFile, inputfile, outputfile))
         scores <- read.table(outputfile)[,1]
         scores <- scores/100
         df$score[good] <- scores

diff --git a/R/getDeepSpCas9Scores.R b/R/getDeepSpCas9Scores.R
@@ -72,7 +72,8 @@ getDeepSpCas9Scores <- function(sequences,
 
     # Ready to get the scores
     env <- basilisk::obtainEnvironmentPath(env_deepspcas9)
-    basilisk.utils::activateEnvironment(env)
+    envls <- basilisk.utils::activateEnvironment(env)
+    on.exit(basilisk.utils::deactivateEnvironment(envls))
     programFile <- system.file("python",
                                "deepspcas9/getDeepSpCas9Scores.py",
                                package="crisprScore",
@@ -81,14 +82,15 @@ getDeepSpCas9Scores <- function(sequences,
                             "deepspcas9/DeepCas9_Final",
                             package="crisprScore")
     modelDir <- paste0(modelDir, "/")
-    cmd <- paste0("python ",
-                  programFile, " ",
-                  inputfile, " ",
-                  modelDir, " ",
-                  outputfile)
+    #cmd <- paste0("python ",
+    #              programFile, " ",
+    #              inputfile, " ",
+    #              modelDir, " ",
+    #              outputfile)
     if (sum(good)>0){
         .dumpToFile(sequences.valid, inputfile)
-        system(cmd)
+        system2("python",
+                c(programFile, inputfile, modelDir, outputfile))
         scores <- read.table(outputfile)[,1]
         #scores <- read.table(outputfile)
         scores <- scores/100

diff --git a/R/getLindelScores.R b/R/getLindelScores.R
@@ -81,7 +81,9 @@ getLindelScores <- function(sequences, fork=FALSE){
                           seq, " ",
                           weights_file, " ",
                           file.full)
-            system(cmd, ignore.stdout=TRUE, ignore.stderr=FALSE)
+            system(cmd,
+                   ignore.stdout=TRUE,
+                   ignore.stderr=FALSE)
             outputs <- list.files(dir)
             outputs <- outputs[grepl(file, outputs)]
             file.remove(file.path(dir,outputs))

diff --git a/R/getRuleSet3Scores.R b/R/getRuleSet3Scores.R
@@ -86,24 +86,27 @@ getRuleSet3Scores <- function(sequences,
 
     # Ready to get the scores
     env <- basilisk::obtainEnvironmentPath(env_rs3)
-    basilisk.utils::activateEnvironment(env)
+    envls <- basilisk.utils::activateEnvironment(env)
+    on.exit(basilisk.utils::deactivateEnvironment(envls))
     programFile <- system.file("python",
                                "rs3/getRuleSet3ScoresSequence.py",
                                package="crisprScore",
                                mustWork=TRUE)
     modelFile <- system.file("rs3",
                              "RuleSet3.pkl",
                              package="crisprScoreData")
-    cmd <- paste0("python ",
-                  programFile, " ",
-                  inputfile, " ",
-                  modelFile, " ",
-                  outputfile, " ",
-                  shQuote(tracrRNA))
+    #cmd <- paste0("python ",
+    #              programFile, " ",
+    #             inputfile, " ",
+    #              modelFile, " ",
+    #              outputfile, " ",
+    #              shQuote(tracrRNA))
     if (sum(good)>0){
         .dumpToFile(sequences.valid,
                     inputfile)
-        system(cmd)
+        system2("python",
+                c(programFile, inputfile, modelFile, 
+                  outputfile,shQuote(tracrRNA)))
         #scores <- readLines(outputfile, sep="\t")[,4]
         scores <- readLines(outputfile)
         df$score[good] <- scores