Mercurial > repos > george-weingart > maaslin
comparison src/test-Maaslin/test-Maaslin.R @ 0:e0b5980139d9
maaslin
| author | george-weingart |
|---|---|
| date | Tue, 13 May 2014 22:00:40 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:e0b5980139d9 |
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| 1 c_strDir <- file.path(getwd( ),"..") | |
| 2 | |
| 3 source(file.path(c_strDir,"lib","Constants.R")) | |
| 4 strTestingDirectory = file.path(c_strDir,c_strTestingDirectory) | |
| 5 sScriptMaaslin = file.path( c_strDir, "Maaslin.R" ) | |
| 6 | |
| 7 context("Test Run From Commandline") | |
| 8 | |
| 9 #Input Files | |
| 10 sTestReadConfig = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.read.config") | |
| 11 sTestCustomR = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.R") | |
| 12 sTestMaaslinDirectory = file.path(strTestingDirectory, c_strTemporaryFiles, "testMaaslin") | |
| 13 sTestOutput = file.path(sTestMaaslinDirectory,"TestMaaslin_Summary.txt") | |
| 14 sTestTSV = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.tsv") | |
| 15 #Test file answers | |
| 16 sTestOutputAnswer = file.path(strTestingDirectory, c_strCorrectAnswers, "TestMaaslin.tsv") | |
| 17 | |
| 18 #Delete Test MaAsLin output | |
| 19 unlink(sTestMaaslinDirectory, recursive=TRUE) | |
| 20 #Make neccessary directories | |
| 21 dir.create(sTestMaaslinDirectory) | |
| 22 dir.create(file.path(sTestMaaslinDirectory,"QC")) | |
| 23 | |
| 24 sCommand = paste(sScriptMaaslin, "-v", "ERROR", "-d", "0.25", "-r", "0.0001", "-p", "0.1", sTestOutput, sTestTSV, sTestReadConfig, sTestCustomR, sep=" ") | |
| 25 print(sCommand) | |
| 26 system(sCommand) | |
| 27 | |
| 28 sExpectedTitle = "\tVariable\tFeature\tValue\tCoefficient\tN\tN.not.0\tP.value\tQ.value" | |
| 29 iExpectedNumberOfLines = 3 | |
| 30 lsOutputSummaryFile = readLines(sTestOutput) | |
| 31 | |
| 32 test_that("Make sure that the summary output file is what is expected (generally).",{ | |
| 33 expect_equal(lsOutputSummaryFile[1], sExpectedTitle) | |
| 34 expect_equal(length(lsOutputSummaryFile),iExpectedNumberOfLines) | |
| 35 }) | |
| 36 | |
| 37 lsDirectoryStructure = list.files(sTestMaaslinDirectory) | |
| 38 lsDirectoryStructureAnswer = c(basename(sTestOutput),"QC","TestMaaslin-age.pdf","TestMaaslin-age.txt","TestMaaslin-dx.txt","TestMaaslin.pdf","TestMaaslin.txt") | |
| 39 test_that("Make sure the expected directory structure is created.",{ | |
| 40 expect_equal(sort(lsDirectoryStructure), sort(lsDirectoryStructureAnswer)) | |
| 41 }) |