Mercurial > repos > george-weingart > maaslin
view maaslin-4450aa4ecc84/maaslin-4450aa4ecc84/SConscript @ 6:ca61989bc3b4
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author | george-weingart |
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date | Sun, 08 Feb 2015 23:39:43 -0500 |
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import sfle import csv Import( "*" ) pE = DefaultEnvironment( ) # Extensions sGraphlanAnnotationFileExtension = "-ann.txt" sGraphlanCoreAnnotFileExtension = "-ann-core.txt" sGraphlanCoreGenesFileExtension = "-core.txt" sGraphlanFigureExtension = "-graphlan.pdf" sMaaslinDataFileExtension = ".txt" sMaaslinReadConfigFileExtension = ".read.config" sMaaslinSummaryFileExtension = ".txt" sCustomRScriptExtension = ".R" sPCLExtension = ".pcl" sTransposeExtension = ".tsv" # Files strMaaslinGraphlanSettings = "Graphlan_settings.txt" # Script sScriptGraphlan = File(os.path.join("..","graphlan","graphlan.py")) sScriptGraphlanAnnotate = File(os.path.join("..","graphlan","graphlan_annotate.py")) sScriptMaaslinSummaryToGraphlanAnnotation = File(sfle.d(fileDirSrc,"MaaslinToGraphlanAnnotation.py")) sScriptPCLToCoreGene = File(sfle.d(fileDirSrc,"PCLToGraphlanCoreGene.py")) sProgMaaslin = sfle.d(fileDirSrc,"Maaslin.R") # Settings iGraphlanDPI = 150 iGraphlanFigureSize = 4 iGraphlanPad = 0.2 strGraphlanDirectory = "graphlan" c_fileDirLib = sfle.d( fileDirSrc, "lib" ) c_fileInputMaaslinR = sfle.d( pE, fileDirSrc, "Maaslin.R" ) c_afileTestsR = [sfle.d( pE, c_fileDirLib, s ) for s in ("IO.R", "SummarizeMaaslin.R", "Utility.R", "ValidateData.R")] c_afileDocsR = c_afileTestsR + [sfle.d( pE, c_fileDirLib, s ) for s in ( "AnalysisModules.R", "scriptBiplotTSV.R", "BoostGLM.R", "Constants.R", "MaaslinPlots.R")] ##Test scripts for fileInputR in c_afileTestsR: strBase = sfle.rebase( fileInputR, True ) #Testing summary file fileTestingSummary = sfle.d( pE, fileDirOutput, strBase +"-TestReport.txt" ) dirTestingR = Dir( sfle.d( fileDirSrc, "test-" + strBase ) ) Default( sfle.testthat( pE, fileInputR, dirTestingR, fileTestingSummary ) ) ##Inline doc for fileProg in c_afileDocsR: filePDF = sfle.d( pE, fileDirOutput, sfle.rebase( fileProg, sfle.c_strSufR, sfle.c_strSufPDF ) ) Default( sfle.inlinedocs( pE, fileProg, filePDF, fileDirTmp ) ) ##Start regression suite execfile( "SConscript_maaslin.py" ) ##Input pcl files lsMaaslinInputFiles = Glob( sfle.d( fileDirInput, "*" + sfle.c_strSufPCL ) ) ## Run MaAsLin and generate output for strPCLFile in lsMaaslinInputFiles: Default( MaAsLin( strPCLFile )) # #Graphlan figure # #TODO Fix path dependent, better way to know it is installed? # if(os.path.exists(sScriptGraphlan.get_abspath())): # ## Run Graphlan on all output projects # strProjectName = os.path.splitext(os.path.split(strPCLFile.get_abspath())[1])[0] # strMaaslinOutputDir = sfle.d(fileDirOutput,strProjectName) # ##Get maaslin data files # strMaaslinSummaryFile = sfle.d(os.path.join(strMaaslinOutputDir, strProjectName + sMaaslinSummaryFileExtension)) # # Make core gene file # sCoreGeneFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanCoreGenesFileExtension)))) # sReadConfigFile = File(sfle.d(fileDirInput,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sMaaslinReadConfigFileExtension))) # sfle.op(pE, sScriptPCLToCoreGene, [[False, strPCLFile],[False, sReadConfigFile],[True, sCoreGeneFile]]) # # Make annotation file # sAnnotationFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanAnnotationFileExtension)))) # sfle.op(pE, sScriptMaaslinSummaryToGraphlanAnnotation, [[False, strMaaslinSummaryFile],[False,sCoreGeneFile],[False,File(sfle.d(fileDirSrc,strMaaslinGraphlanSettings))],[True,sAnnotationFile]]) # # Generate core gene annotation file names # sCoreGeneAnnotationFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanCoreAnnotFileExtension)))) # sfle.op(pE, sScriptGraphlanAnnotate, ["--annot",[sAnnotationFile],[False, sCoreGeneFile],[True, sCoreGeneAnnotationFile]]) # # Call graphlan # # graphlan.py --dpi 150 --size 4 --pad 0.2 core_genes.annot.xml core_genes.png # sGraphlanFigure = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory, sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanFigureExtension)))) # sfle.op(pE, sScriptGraphlan, [[False, sCoreGeneAnnotationFile],[True, sGraphlanFigure],"--dpi",iGraphlanDPI,"--size",iGraphlanFigureSize,"--pad",iGraphlanPad]) # Default(sCoreGeneFile,sAnnotationFile,sCoreGeneAnnotationFile,sGraphlanFigure)