tests/testthat/testImportSNV.TCGA.R

In hyginn/ekplektoR: Network Analysis for Cell- and Systems Biology

# # testImportSNV.TCGA.R
#
# # ==== BEGIN SETUP AND PREPARE =================================================
# OLOG <- as.character(getOption("rete.logfile"))   # save original logfile name
# logFileName(fPath = tempdir(), setOption = TRUE)  # make tempdir() the log dir
# NL <- .PlatformLineBreak
# # ==== END SETUP AND PREPARE ===================================================
#
# #context("Tools for importing MAF files into a rSNV file")
# options(stringsAsFactors=FALSE)
# testIN <- "importSNV_input_test_file.maf"
# testOUT <- "importSNV_output_test_file"
# testINcorr <- "importSNV_input_corr_file.maf"
#
# test_that("parameter errors are correctly handled", {
#     testMAF <- tempfile()
#     tOut <- tempfile()
#     trueIn <- data.frame()
#     input0 <- c("Hugo_Symbol" , "Entrez_Gene_Id" , "Center" , "NCBI_Build" , "Chromosome" , "Start_Position" , "End_Position" , "Strand" , "Variant_Classification" , "Variant_Type" , "Reference_Allele" , "Tumor_Seq_Allele1" , "Tumor_Seq_Allele2" , "dbSNP_RS" , "dbSNP_Val_Status" , "Tumor_Sample_Barcode" , "Matched_Norm_Sample_Barcode" , "Match_Norm_Seq_Allele1" , "Match_Norm_Seq_Allele2" , "Tumor_Validation_Allele1" , "Tumor_Validation_Allele2" , "Match_Norm_Validation_Allele1" , "Match_Norm_Validation_Allele2" , "Verification_Status" , "Validation_Status" , "Mutation_Status" )
#     input1 <- c("TMEM201" , 199953 , "WUGSC" , "GRCh38" , "chr1" , 9607661 , 9607661 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09" , "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a", "c.1265C>T" , "p.Pro422Leu", "p.P422L" , "ENST00000340381")
#     input2 <- c("PTCHD2" , 57540 , "WUGSC" , "GRCh38" , "chr1" , 11516130 , 11516130 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09" , "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a" , "c.1718C>T" , "p.Ala573Val" , "p.A573V" , "ENST00000294484")
#     input3 <- c("VWA5B1" , 127731 , "WUGSC" , "GRCh38" , "chr1" , 20319393 , 20319393 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09", "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a" , "c.853C>T" , "p.Pro285Ser" , "p.P285S" , "ENST00000375079")
#
#     trueIn <- rbind(input0, input1, input2, input3)
#
#     write.table(trueIn,  file=testMAF, sep="\t", append=FALSE, row.names =
#                     FALSE, col.names = FALSE, quote = FALSE)
#     # fMAF is not provided
#     expect_error(importSNV.TCGA(), "argument \"fMAF\" is missing, with no default")
#     # fMAF is NULL/empty vector
#     expect_error(importSNV.TCGA(fMAF = NULL, tOut), ".checkArgs> \"fMAF\" mode error: argument has mode \"NULL\" but function expects mode \"character\".")
#     # fMAF input vector contains non-string values
#     expect_error(importSNV.TCGA(fMAF = 123, tOut), ".checkArgs> \"fMAF\" mode error: argument has mode \"numeric\" but function expects mode \"character\".")
#
#     # rSNV is missing
#     expect_error(importSNV.TCGA(fMAF = testMAF), "argument \"rSNV\" is missing, with no default")
#     # if rSNV parameter is provided, but is NULL
#     expect_error(importSNV.TCGA(fMAF = testMAF, rSNV = NULL), ".checkArgs> \"rSNV\" mode error: argument has mode \"NULL\" but function expects mode \"character\".")
#     # if rSNV parameter is provided, but is non-string value
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, rSNV = 123), ".checkArgs> \"rSNV\" mode error: argument has mode \"numeric\" but function expects mode \"character\".")
#     # if rSNV is given vector input
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, rSNV = c("abc", "xyz")), ".checkArgs> \"rSNV\" length error: argument has length 2 but function expects length 1.")
#
#     # if silent is not given logical input
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = 1), ".checkArgs> \"silent\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = NULL), ".checkArgs> \"silent\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = c(TRUE, TRUE)), ".checkArgs> \"silent\" length error: argument has length 2 but function expects length 1.")
#
#     # writeLog is not given logical input
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = 1), ".checkArgs> \"writeLog\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = NULL), ".checkArgs> \"writeLog\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = c(TRUE, TRUE)), ".checkArgs> \"writeLog\" length error: argument has length 2 but function expects length 1.")
#
#     # if na.rm is not given logical input
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = 1), ".checkArgs> \"na.rm\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = NULL), ".checkArgs> \"na.rm\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = c(TRUE, TRUE)), ".checkArgs> \"na.rm\" length error: argument has length 2 but function expects length 1.")
#     # ToDo - confirm that no log file was written.
#     expect_true(file.remove(testMAF))
# })
#
# test_that("a sane input gives an expected output with different input parameters", {
#
#     tOut <- tempfile()
#     tOut1 <- tempfile()
#     tOut2 <- tempfile()
#     trueOut <- data.frame()
#
#     # MAKE SMALL OUTPUT (trueOut) --------------------------------------------------
#     trueOut <- read.table(testOUT, sep = "\t", stringsAsFactors = FALSE)
#
#     # run the module on only fMAF and rSNV as parameters (moduleOut)
#     importSNV.TCGA(testIN, tOut, writeLog = FALSE)
#     # check if manual output = module output
#     module <- read.table(tOut, sep = "\t", stringsAsFactors = FALSE)
#
#     # TEST fMAF parameter ==========================================================
#     expect_equal(trueOut, module)
#     #===============================================================================
#
#     # TEST fMAF, rSNV, silent parameters ============================================
#     # run the module on fMAF and rSNV and silent as parameters
#     importSNV.TCGA(testIN, tOut1, silent=TRUE, writeLog = FALSE)
#     modulePre2 <- read.table(tOut1, sep = "\t", stringsAsFactors = FALSE)
#     # add to prexisting rSNV file
#     expect_equal(trueOut, modulePre2)
#     #===============================================================================
#
#     # TEST fMAF, rSNV, silent, writeLog parameters =================================
#     # run the module on fMAF, rSNV, silent and writeLog as parameters
#     importSNV.TCGA(testIN, tOut2, silent=FALSE, writeLog=FALSE)
#     modulePre3 <- read.table(tOut2, sep = "\t", stringsAsFactors = FALSE)
#     # add to prexisting rSNV file
#     expect_equal(trueOut, modulePre3)
#     #===============================================================================
#
#     # test input with rSNV as input and NA values -------------------------------------------
#     tOut3 <- tempfile()
#
#     # TEST fMAF, rSNV, silent, writeLog parameters, na.rm ==========================
#     # run the module on fMAF, rSNV, silent, writeLog and na.rm as parameters
#     importSNV.TCGA(testIN, tOut3, silent=FALSE, writeLog=FALSE, na.rm=TRUE)
#     moduleNA <- read.table(tOut3, sep = "\t", stringsAsFactors = FALSE)
#     # add to prexisting rSNV file
#     expect_equal(trueOut, moduleNA)
# })
#
#
# test_that("a corrupt input does not lead to corrupted output", {
#     # checking for version is not necessary : can handle all versions (2.4.1(latest) and below)
#     # other forms of corrupted input tested for in importSNV.TCGA.R
#
#     # this is the test for corrupted final line
#     tOut <- tempfile()
#     expect_warning(importSNV.TCGA(testINcorr, tOut), "incomplete final line found by readTableHeader on 'importSNV_input_corr_file.maf'")
# })
#
# test_that("silent and writeLog work as intended", {
#     # if silent=TRUE, check if output to console is supressed
#     tOut <- tempfile()
#     testF <- tempfile()
#     capture.output(importSNV.TCGA(testIN, tOut, silent = TRUE, writeLog = FALSE), file = testF)
#     expect_equal(length(readLines(testF)), 0)
#     expect_true(file.remove(testF))
#
#     # check writeLog works as intended
#     importSNV.TCGA(testIN, tOut, writeLog = TRUE)
#     expect_equal(readLines(unlist(getOption("rete.logfile")))[1], "event | title  | importSNV.TCGA")
# })
#
#
# # ==== BEGIN TEARDOWN AND RESTORE ==============================================
# logName <- unlist(getOption("rete.logfile"))
# if (file.exists(logName)) { file.remove(logName)}
# options("rete.logfile" = OLOG)
# # ==== END  TEARDOWN AND RESTORE ===============================================
# # [END]