Mercurial > repos > george-weingart > maaslin
diff src/test-SummarizeMaaslin/test-SummarizeMaaslin.R @ 0:e0b5980139d9
maaslin
author | george-weingart |
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date | Tue, 13 May 2014 22:00:40 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/test-SummarizeMaaslin/test-SummarizeMaaslin.R Tue May 13 22:00:40 2014 -0400 @@ -0,0 +1,72 @@ +c_strDir <- file.path(getwd( ),"..") + +source(file.path(c_strDir,"lib","Constants.R")) +source(file.path(c_strDir,"lib","SummarizeMaaslin.R")) +source(file.path(c_strDir,"lib","Utility.R")) + +context("Test funcSummarizeDirectory") +strDirectoryNone = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","None") +strDirectory1 = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","1") +strDirectory3 = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","3") +strFileBase1 = "FileBase1.txt" +strFileBase2 = "FileBase2.txt" + +sKeyword = "Q.value" +sAltKeyword = "P.value" +sAltSignificance = "0.35" + +sBaseName = "FuncSummarizeDirectory" + +#Output and answer files +sNoFileResult = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileResult.txt") +sNoFileResultAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileAltKeyResult.txt") +sNoFileResultAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileAltSigResult.txt") +sNoFileResultAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAnswer.txt") +sNoFileResultAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAltKeyAnswer.txt") +sNoFileResultAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAltSigAnswer.txt") +unlink(sNoFileResult) +sCorrectResults1File = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileResult.txt") +sCorrectResults1FileAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileAltKeyResult.txt") +sCorrectResults1FileAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileAltSigResult.txt") +sCorrectResults1FileAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileResult.txt") +sCorrectResults1FileAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileAltKeyResult.txt") +sCorrectResults1FileAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileAltSigResult.txt") +unlink(sCorrectResults1File) +sCorrectResults3Files = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileResult.txt") +sCorrectResults3FilesAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileAltKeyResult.txt") +sCorrectResults3FilesAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileAltSigResult.txt") +sCorrectResults3FilesAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileResult.txt") +sCorrectResults3FilesAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileAltKeyResult.txt") +sCorrectResults3FilesAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileAltSigResult.txt") +unlink(sCorrectResults3Files) + +#Run tests +funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResult, astrKeyword=sKeyword, afSignificanceLevel="0.25") +funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1File, astrKeyword=sKeyword, afSignificanceLevel="0.25") +funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3Files, astrKeyword=sKeyword, afSignificanceLevel="0.25") + +funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResultAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25") +funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1FileAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25") +funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3FilesAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25") + +funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResultAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance) +funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1FileAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance) +funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3FilesAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance) + +test_that("Check the cases where no, and real summary files exist.",{ + expect_equal(readLines(sNoFileResult),readLines(sNoFileResultAnswer)) + expect_equal(readLines(sCorrectResults1File),readLines(sCorrectResults1FileAnswer)) + expect_equal(readLines(sCorrectResults3Files),readLines(sCorrectResults3FilesAnswer)) +}) + +test_that("Check changing the keyword.",{ + expect_equal(readLines(sNoFileResultAltKeyword),readLines(sNoFileResultAnswerAltKeyword)) + expect_equal(readLines(sCorrectResults1FileAltKeyword),readLines(sCorrectResults1FileAnswerAltKeyword)) + expect_equal(readLines(sCorrectResults3FilesAltKeyword),readLines(sCorrectResults3FilesAnswerAltKeyword)) +}) + +test_that("Check that changing the significance threshold effects inclusion.",{ + expect_equal(readLines(sNoFileResultAltSig),readLines(sNoFileResultAnswerAltSig)) + expect_equal(readLines(sCorrectResults1FileAltSig),readLines(sCorrectResults1FileAnswerAltSig)) + expect_equal(readLines(sCorrectResults3FilesAltSig),readLines(sCorrectResults3FilesAnswerAltSig)) +})