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comparison src/test-SummarizeMaaslin/test-SummarizeMaaslin.R @ 0:e0b5980139d9

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maaslin
author george-weingart
date Tue, 13 May 2014 22:00:40 -0400
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-1:000000000000 0:e0b5980139d9
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 })