1. crisprScore
  2. Commit 4af68d2d9fc4c6673a79653f890fb97aa1ba0e1c
Browse code

Changed system to system2

fortinj2 authored on 19/07/2022 21:53:01
Showing 6 changed files
NAMESPACE
History View file @ 4af68d2
... ... 
@@ -36,6 +36,7 @@ importFrom(basilisk,basiliskStop)
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 importFrom(basilisk,obtainEnvironmentPath)
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 importFrom(basilisk,setBasiliskFork)
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 importFrom(basilisk.utils,activateEnvironment)
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+importFrom(basilisk.utils,deactivateEnvironment)
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 importFrom(methods,is)
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 importFrom(randomForest,randomForest)
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 importFrom(reticulate,import_from_path)
R/getAzimuthScores.R
History View file @ 4af68d2
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@@ -67,22 +67,24 @@ getAzimuthScores <- function(sequences, fork=FALSE){
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       # Ready to get the scores
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     env <- basilisk::obtainEnvironmentPath(env_azimuth)
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-    basilisk.utils::activateEnvironment(env)
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+    envls <- basilisk.utils::activateEnvironment(env)
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+    on.exit(basilisk.utils::deactivateEnvironment(envls))
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     programFile <- system.file("python",
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                                "azimuth/getAzimuth.py",
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                                package="crisprScore",
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                                mustWork=TRUE)
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-    cmd <- paste0("python ",
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-                  programFile, " ",
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-                  inputfile, " ",
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-                  outputfile)
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+    #cmd <- paste0("python ",
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+    #              programFile, " ",
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+    #              inputfile, " ",
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+    #              outputfile)
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     if (sum(good)>0){
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         if (sum(good)==1){
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             sequences.valid <- rep(sequences.valid, 2)
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         }
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         .dumpToFile(sequences.valid, inputfile)
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-        system(cmd)
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+        system2("python",
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+                c(programFile, inputfile, outputfile))
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         scores <- read.table(outputfile)[,1]
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         if (sum(good)==1){
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             scores <- scores[1]
R/getDeepCpf1Scores.R
History View file @ 4af68d2
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@@ -39,9 +39,13 @@
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 #' @inheritParams getAzimuthScores
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 #' @export
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 #' @importFrom basilisk basiliskStart basiliskStop basiliskRun
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+#' @importFrom basilisk.utils activateEnvironment
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+#' @importFrom basilisk.utils deactivateEnvironment
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 getDeepCpf1Scores <- function(sequences,
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                               convertPAM=TRUE,
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-                              fork=FALSE){
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+                              fork=FALSE
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+){
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+
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     if (.Platform$OS.type=="windows"){
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         stop("DeepCpf1 is not available for Windows at the moment.")
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     }
... ... 
@@ -74,18 +78,21 @@ getDeepCpf1Scores <- function(sequences,
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     # Ready to get the scores
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     env <- basilisk::obtainEnvironmentPath(env_deepcpf1)
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-    basilisk.utils::activateEnvironment(env)
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+    envls <- basilisk.utils::activateEnvironment(env)
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+    on.exit(basilisk.utils::deactivateEnvironment(envls))
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     programFile <- system.file("python",
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                                "deepcpf1/getDeepCpf1.py",
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                                package="crisprScore",
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                                mustWork=TRUE)
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-    cmd <- paste0("python ",
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-                  programFile, " ",
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-                  inputfile, " ",
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-                  outputfile)
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+    #cmd <- paste0("python ",
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+    #              programFile, " ",
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+    #              inputfile, " ",
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+    #              outputfile)
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     if (sum(good)>0){
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         .dumpToFile(sequences.valid, inputfile)
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-        system(cmd)
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+        #system(cmd)
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+        system2("python",
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+                c(programFile, inputfile, outputfile))
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         scores <- read.table(outputfile)[,1]
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         scores <- scores/100
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         df$score[good] <- scores
R/getDeepSpCas9Scores.R
History View file @ 4af68d2
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@@ -72,7 +72,8 @@ getDeepSpCas9Scores <- function(sequences,
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     # Ready to get the scores
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     env <- basilisk::obtainEnvironmentPath(env_deepspcas9)
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-    basilisk.utils::activateEnvironment(env)
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+    envls <- basilisk.utils::activateEnvironment(env)
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+    on.exit(basilisk.utils::deactivateEnvironment(envls))
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     programFile <- system.file("python",
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                                "deepspcas9/getDeepSpCas9Scores.py",
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                                package="crisprScore",
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@@ -81,14 +82,15 @@ getDeepSpCas9Scores <- function(sequences,
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                             "deepspcas9/DeepCas9_Final",
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                             package="crisprScore")
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     modelDir <- paste0(modelDir, "/")
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-    cmd <- paste0("python ",
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-                  programFile, " ",
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-                  inputfile, " ",
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-                  modelDir, " ",
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-                  outputfile)
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+    #cmd <- paste0("python ",
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+    #              programFile, " ",
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+    #              inputfile, " ",
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+    #              modelDir, " ",
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+    #              outputfile)
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     if (sum(good)>0){
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         .dumpToFile(sequences.valid, inputfile)
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-        system(cmd)
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+        system2("python",
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+                c(programFile, inputfile, modelDir, outputfile))
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         scores <- read.table(outputfile)[,1]
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         #scores <- read.table(outputfile)
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         scores <- scores/100
R/getLindelScores.R
History View file @ 4af68d2
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@@ -81,7 +81,9 @@ getLindelScores <- function(sequences, fork=FALSE){
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                           seq, " ",
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                           weights_file, " ",
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                           file.full)
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-            system(cmd, ignore.stdout=TRUE, ignore.stderr=FALSE)
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+            system(cmd,
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+                   ignore.stdout=TRUE,
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+                   ignore.stderr=FALSE)
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             outputs <- list.files(dir)
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             outputs <- outputs[grepl(file, outputs)]
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             file.remove(file.path(dir,outputs))
R/getRuleSet3Scores.R
History View file @ 4af68d2
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@@ -86,7 +86,8 @@ getRuleSet3Scores <- function(sequences,
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     # Ready to get the scores
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     env <- basilisk::obtainEnvironmentPath(env_rs3)
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-    basilisk.utils::activateEnvironment(env)
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+    envls <- basilisk.utils::activateEnvironment(env)
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+    on.exit(basilisk.utils::deactivateEnvironment(envls))
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     programFile <- system.file("python",
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                                "rs3/getRuleSet3ScoresSequence.py",
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                                package="crisprScore",
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@@ -94,16 +95,18 @@ getRuleSet3Scores <- function(sequences,
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     modelFile <- system.file("rs3",
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                              "RuleSet3.pkl",
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                              package="crisprScoreData")
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-    cmd <- paste0("python ",
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-                  programFile, " ",
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-                  inputfile, " ",
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-                  modelFile, " ",
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-                  outputfile, " ",
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-                  shQuote(tracrRNA))
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+    #cmd <- paste0("python ",
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+    #              programFile, " ",
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+    #             inputfile, " ",
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+    #              modelFile, " ",
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+    #              outputfile, " ",
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+    #              shQuote(tracrRNA))
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     if (sum(good)>0){
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         .dumpToFile(sequences.valid,
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                     inputfile)
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-        system(cmd)
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+        system2("python",
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+                c(programFile, inputfile, modelFile,
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+                  outputfile,shQuote(tracrRNA)))
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         #scores <- readLines(outputfile, sep="\t")[,4]
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         scores <- readLines(outputfile)
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         df$score[good] <- scores