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6
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1 c_strDir <- file.path(getwd( ),"..")
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2
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3 source(file.path(c_strDir,"lib","Constants.R"))
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4 strTestingDirectory = file.path(c_strDir,c_strTestingDirectory)
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5 sScriptMaaslin = file.path( c_strDir, "Maaslin.R" )
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6
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7 context("Test Run From Commandline")
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8
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9 #Input Files
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10 sTestReadConfig = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.read.config")
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11 sTestCustomR = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.R")
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12 sTestMaaslinDirectory = file.path(strTestingDirectory, c_strTemporaryFiles, "testMaaslin")
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13 sTestOutput = file.path(sTestMaaslinDirectory,"TestMaaslin_Summary.txt")
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14 sTestTSV = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.tsv")
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15 #Test file answers
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16 sTestOutputAnswer = file.path(strTestingDirectory, c_strCorrectAnswers, "TestMaaslin.tsv")
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17
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18 #Delete Test MaAsLin output
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19 unlink(sTestMaaslinDirectory, recursive=TRUE)
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20 #Make neccessary directories
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21 dir.create(sTestMaaslinDirectory)
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22 dir.create(file.path(sTestMaaslinDirectory,"QC"))
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23
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24 sCommand = paste(sScriptMaaslin, "-v", "ERROR", "-d", "0.25", "-r", "0.0001", "-p", "0.1", sTestOutput, sTestTSV, sTestReadConfig, sTestCustomR, sep=" ")
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25 print(sCommand)
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26 system(sCommand)
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27
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28 sExpectedTitle = "\tVariable\tFeature\tValue\tCoefficient\tN\tN.not.0\tP.value\tQ.value"
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29 iExpectedNumberOfLines = 3
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30 lsOutputSummaryFile = readLines(sTestOutput)
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31
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32 test_that("Make sure that the summary output file is what is expected (generally).",{
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33 expect_equal(lsOutputSummaryFile[1], sExpectedTitle)
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34 expect_equal(length(lsOutputSummaryFile),iExpectedNumberOfLines)
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35 })
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36
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37 lsDirectoryStructure = list.files(sTestMaaslinDirectory)
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38 lsDirectoryStructureAnswer = c(basename(sTestOutput),"QC","TestMaaslin-age.pdf","TestMaaslin-age.txt","TestMaaslin-dx.txt","TestMaaslin.pdf","TestMaaslin.txt")
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39 test_that("Make sure the expected directory structure is created.",{
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40 expect_equal(sort(lsDirectoryStructure), sort(lsDirectoryStructureAnswer))
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41 })
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