|
0
|
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 })
|
