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1 import sfle
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2 import csv
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3
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4 Import( "*" )
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5 pE = DefaultEnvironment( )
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6
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7 # Extensions
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8 sGraphlanAnnotationFileExtension = "-ann.txt"
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9 sGraphlanCoreAnnotFileExtension = "-ann-core.txt"
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10 sGraphlanCoreGenesFileExtension = "-core.txt"
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11 sGraphlanFigureExtension = "-graphlan.pdf"
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12 sMaaslinDataFileExtension = ".txt"
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13 sMaaslinReadConfigFileExtension = ".read.config"
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14 sMaaslinSummaryFileExtension = ".txt"
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15
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16 sCustomRScriptExtension = ".R"
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17 sPCLExtension = ".pcl"
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18 sTransposeExtension = ".tsv"
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19
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20 # Files
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21 strMaaslinGraphlanSettings = "Graphlan_settings.txt"
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22
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23 # Script
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24 sScriptGraphlan = File(os.path.join("..","graphlan","graphlan.py"))
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25 sScriptGraphlanAnnotate = File(os.path.join("..","graphlan","graphlan_annotate.py"))
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26 sScriptMaaslinSummaryToGraphlanAnnotation = File(sfle.d(fileDirSrc,"MaaslinToGraphlanAnnotation.py"))
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27 sScriptPCLToCoreGene = File(sfle.d(fileDirSrc,"PCLToGraphlanCoreGene.py"))
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28
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29 sProgMaaslin = sfle.d(fileDirSrc,"Maaslin.R")
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30
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31 # Settings
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32 iGraphlanDPI = 150
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33 iGraphlanFigureSize = 4
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34 iGraphlanPad = 0.2
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35 strGraphlanDirectory = "graphlan"
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36
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37 c_fileDirLib = sfle.d( fileDirSrc, "lib" )
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38 c_fileInputMaaslinR = sfle.d( pE, fileDirSrc, "Maaslin.R" )
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39 c_afileTestsR = [sfle.d( pE, c_fileDirLib, s ) for s in
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40 ("IO.R", "SummarizeMaaslin.R", "Utility.R", "ValidateData.R")]
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41
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42 c_afileDocsR = c_afileTestsR + [sfle.d( pE, c_fileDirLib, s ) for s in
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43 ( "AnalysisModules.R", "scriptBiplotTSV.R", "BoostGLM.R", "Constants.R", "MaaslinPlots.R")]
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44
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45 ##Test scripts
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46 for fileInputR in c_afileTestsR:
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47 strBase = sfle.rebase( fileInputR, True )
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48 #Testing summary file
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49 fileTestingSummary = sfle.d( pE, fileDirOutput, strBase +"-TestReport.txt" )
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50 dirTestingR = Dir( sfle.d( fileDirSrc, "test-" + strBase ) )
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51 Default( sfle.testthat( pE, fileInputR, dirTestingR, fileTestingSummary ) )
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52
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53 ##Inline doc
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54 for fileProg in c_afileDocsR:
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55 filePDF = sfle.d( pE, fileDirOutput, sfle.rebase( fileProg, sfle.c_strSufR, sfle.c_strSufPDF ) )
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56 Default( sfle.inlinedocs( pE, fileProg, filePDF, fileDirTmp ) )
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57
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58 ##Start regression suite
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59 execfile( "SConscript_maaslin.py" )
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60
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61 ##Input pcl files
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62 lsMaaslinInputFiles = Glob( sfle.d( fileDirInput, "*" + sfle.c_strSufPCL ) )
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63
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64 ## Run MaAsLin and generate output
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65 for strPCLFile in lsMaaslinInputFiles:
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66 Default( MaAsLin( strPCLFile ))
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67
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68 # #Graphlan figure
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69 # #TODO Fix path dependent, better way to know it is installed?
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70 # if(os.path.exists(sScriptGraphlan.get_abspath())):
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71
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72 # ## Run Graphlan on all output projects
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73 # strProjectName = os.path.splitext(os.path.split(strPCLFile.get_abspath())[1])[0]
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74 # strMaaslinOutputDir = sfle.d(fileDirOutput,strProjectName)
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75
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76 # ##Get maaslin data files
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77 # strMaaslinSummaryFile = sfle.d(os.path.join(strMaaslinOutputDir, strProjectName + sMaaslinSummaryFileExtension))
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78
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79 # # Make core gene file
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80 # sCoreGeneFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanCoreGenesFileExtension))))
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81 # sReadConfigFile = File(sfle.d(fileDirInput,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sMaaslinReadConfigFileExtension)))
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82 # sfle.op(pE, sScriptPCLToCoreGene, [[False, strPCLFile],[False, sReadConfigFile],[True, sCoreGeneFile]])
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83
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84 # # Make annotation file
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85 # sAnnotationFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanAnnotationFileExtension))))
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86 # sfle.op(pE, sScriptMaaslinSummaryToGraphlanAnnotation, [[False, strMaaslinSummaryFile],[False,sCoreGeneFile],[False,File(sfle.d(fileDirSrc,strMaaslinGraphlanSettings))],[True,sAnnotationFile]])
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87
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88 # # Generate core gene annotation file names
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89 # sCoreGeneAnnotationFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanCoreAnnotFileExtension))))
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90 # sfle.op(pE, sScriptGraphlanAnnotate, ["--annot",[sAnnotationFile],[False, sCoreGeneFile],[True, sCoreGeneAnnotationFile]])
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91
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92 # # Call graphlan
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93 # # graphlan.py --dpi 150 --size 4 --pad 0.2 core_genes.annot.xml core_genes.png
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94 # sGraphlanFigure = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory, sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanFigureExtension))))
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95 # sfle.op(pE, sScriptGraphlan, [[False, sCoreGeneAnnotationFile],[True, sGraphlanFigure],"--dpi",iGraphlanDPI,"--size",iGraphlanFigureSize,"--pad",iGraphlanPad])
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96
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97 # Default(sCoreGeneFile,sAnnotationFile,sCoreGeneAnnotationFile,sGraphlanFigure)
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