diff runit/batchcorrection_runtests.R @ 3:2e3a23dd6c24 draft default tip

Uploaded

--- a/runit/batchcorrection_runtests.R	Mon May 01 08:06:08 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,130 +0,0 @@
-#!/usr/bin/env Rscript
-
-## Package
-##--------
-
-library(RUnit)
-
-## Constants
-##----------
-
-testOutDirC <- "output"
-argVc <- commandArgs(trailingOnly = FALSE)
-scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
-
-
-## Functions
-##-----------
-
-## Reading tables (matrix or data frame)
-readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
-
-    	file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
-
-        switch(typeC,
-               matrix = return(t(as.matrix(read.table(file = fileC,
-                   header = TRUE,
-                   row.names = 1,
-                   sep = "\t",
-                   stringsAsFactors = FALSE)))),
-               dataframe = return(read.table(file = fileC,
-                   header = TRUE,
-                   row.names = 1,
-                   sep = "\t",
-                   stringsAsFactors = FALSE)))
-
-}
-
-## Call wrapper
-wrapperCallF <- function(paramLs, allLoessL) {
-
-    ## Set program path
-    wrapperPathC <- file.path(dirname(scriptPathC), "..",
-                              ifelse(allLoessL,
-                                     "batch_correction_all_loess_wrapper.R",
-                                     "batch_correction_wrapper.R"))
-
-    ## Set arguments
-    argLs <- NULL
-    for (parC in names(paramLs))
-        argLs <- c(argLs, parC, paramLs[[parC]])
-
-    ## Call
-    wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
-
-    if(.Platform$OS.type == "windows")
-        wrapperCallC <- paste("Rscript", wrapperCallC)
-
-
-    print(wrapperCallC)
-    
-
-    wrapperCodeN <- system(wrapperCallC)
-
-    if (wrapperCodeN != 0)
-        stop(paste0("Error when running 'batch_correction_",
-                    ifelse(allLoessL, "all_loess_", ""),
-                    "wrapper.R'"))
-
-    ## Get output
-    outLs <- list()
-    if ("dataMatrix_out" %in% names(paramLs))
-        outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
-    if ("sampleMetadata_out" %in% names(paramLs))
-        outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
-    if ("variableMetadata_out" %in% names(paramLs))
-        outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
-    if("information" %in% names(paramLs))
-        outLs[["infVc"]] <- readLines(paramLs[["information"]])
-
-    if("out_preNormSummary" %in% names(paramLs))
-        outLs[["sumDF"]] <- readTableF(paramLs[["out_preNormSummary"]], "dataframe")
-
-    return(outLs)
-    
-}
-
-## Setting default parameters
-defaultArgF <- function(testInDirC, determineL) {
-
-    defaultArgLs <- list()
-
-    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
-        defaultArgLs[["dataMatrix"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
-    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
-        defaultArgLs[["sampleMetadata"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
-
-    if(!determineL)
-        if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
-            defaultArgLs[["variableMetadata"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
-
-    if(determineL) { ## determinebc
-
-        defaultArgLs[["out_graph_pdf"]] <- file.path(dirname(scriptPathC), testOutDirC, "out_graph.pdf")
-        defaultArgLs[["out_preNormSummary"]] <- file.path(dirname(scriptPathC), testOutDirC, "preNormSummary.txt")
-
-    } else { ## batchcorrection
-        
-        defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv")
-        defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
-        defaultArgLs[["graph_output"]] <- file.path(dirname(scriptPathC), testOutDirC, "graph_output.pdf")
-        defaultArgLs[["rdata_output"]] <- file.path(dirname(scriptPathC), testOutDirC, "rdata_output.rdata")
-        
-       }
-
-    defaultArgLs
-
-}
-
-## Main
-##-----
-
-## Create output folder
-file.exists(testOutDirC) || dir.create(testOutDirC)
-
-## Run tests
-test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
-isValidTestSuite(test.suite)
-test.results <- runTestSuite(test.suite)
-print(test.results)
-