Mercurial > repos > george-weingart > maaslin
comparison maaslin-4450aa4ecc84/src/test-SummarizeMaaslin/test-SummarizeMaaslin.R @ 1:a87d5a5f2776
Uploaded the version running on the prod server
| author | george-weingart |
|---|---|
| date | Sun, 08 Feb 2015 23:08:38 -0500 |
| parents | |
| children |
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| 0:e0b5980139d9 | 1:a87d5a5f2776 |
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| 1 c_strDir <- file.path(getwd( ),"..") | |
| 2 | |
| 3 source(file.path(c_strDir,"lib","Constants.R")) | |
| 4 source(file.path(c_strDir,"lib","SummarizeMaaslin.R")) | |
| 5 source(file.path(c_strDir,"lib","Utility.R")) | |
| 6 | |
| 7 context("Test funcSummarizeDirectory") | |
| 8 strDirectoryNone = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","None") | |
| 9 strDirectory1 = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","1") | |
| 10 strDirectory3 = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","3") | |
| 11 strFileBase1 = "FileBase1.txt" | |
| 12 strFileBase2 = "FileBase2.txt" | |
| 13 | |
| 14 sKeyword = "Q.value" | |
| 15 sAltKeyword = "P.value" | |
| 16 sAltSignificance = "0.35" | |
| 17 | |
| 18 sBaseName = "FuncSummarizeDirectory" | |
| 19 | |
| 20 #Output and answer files | |
| 21 sNoFileResult = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileResult.txt") | |
| 22 sNoFileResultAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileAltKeyResult.txt") | |
| 23 sNoFileResultAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileAltSigResult.txt") | |
| 24 sNoFileResultAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAnswer.txt") | |
| 25 sNoFileResultAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAltKeyAnswer.txt") | |
| 26 sNoFileResultAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAltSigAnswer.txt") | |
| 27 unlink(sNoFileResult) | |
| 28 sCorrectResults1File = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileResult.txt") | |
| 29 sCorrectResults1FileAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileAltKeyResult.txt") | |
| 30 sCorrectResults1FileAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileAltSigResult.txt") | |
| 31 sCorrectResults1FileAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileResult.txt") | |
| 32 sCorrectResults1FileAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileAltKeyResult.txt") | |
| 33 sCorrectResults1FileAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileAltSigResult.txt") | |
| 34 unlink(sCorrectResults1File) | |
| 35 sCorrectResults3Files = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileResult.txt") | |
| 36 sCorrectResults3FilesAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileAltKeyResult.txt") | |
| 37 sCorrectResults3FilesAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileAltSigResult.txt") | |
| 38 sCorrectResults3FilesAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileResult.txt") | |
| 39 sCorrectResults3FilesAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileAltKeyResult.txt") | |
| 40 sCorrectResults3FilesAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileAltSigResult.txt") | |
| 41 unlink(sCorrectResults3Files) | |
| 42 | |
| 43 #Run tests | |
| 44 funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResult, astrKeyword=sKeyword, afSignificanceLevel="0.25") | |
| 45 funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1File, astrKeyword=sKeyword, afSignificanceLevel="0.25") | |
| 46 funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3Files, astrKeyword=sKeyword, afSignificanceLevel="0.25") | |
| 47 | |
| 48 funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResultAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25") | |
| 49 funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1FileAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25") | |
| 50 funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3FilesAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25") | |
| 51 | |
| 52 funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResultAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance) | |
| 53 funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1FileAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance) | |
| 54 funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3FilesAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance) | |
| 55 | |
| 56 test_that("Check the cases where no, and real summary files exist.",{ | |
| 57 expect_equal(readLines(sNoFileResult),readLines(sNoFileResultAnswer)) | |
| 58 expect_equal(readLines(sCorrectResults1File),readLines(sCorrectResults1FileAnswer)) | |
| 59 expect_equal(readLines(sCorrectResults3Files),readLines(sCorrectResults3FilesAnswer)) | |
| 60 }) | |
| 61 | |
| 62 test_that("Check changing the keyword.",{ | |
| 63 expect_equal(readLines(sNoFileResultAltKeyword),readLines(sNoFileResultAnswerAltKeyword)) | |
| 64 expect_equal(readLines(sCorrectResults1FileAltKeyword),readLines(sCorrectResults1FileAnswerAltKeyword)) | |
| 65 expect_equal(readLines(sCorrectResults3FilesAltKeyword),readLines(sCorrectResults3FilesAnswerAltKeyword)) | |
| 66 }) | |
| 67 | |
| 68 test_that("Check that changing the significance threshold effects inclusion.",{ | |
| 69 expect_equal(readLines(sNoFileResultAltSig),readLines(sNoFileResultAnswerAltSig)) | |
| 70 expect_equal(readLines(sCorrectResults1FileAltSig),readLines(sCorrectResults1FileAnswerAltSig)) | |
| 71 expect_equal(readLines(sCorrectResults3FilesAltSig),readLines(sCorrectResults3FilesAnswerAltSig)) | |
| 72 }) |