diff SConscript @ 0:e0b5980139d9

maaslin

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SConscript	Tue May 13 22:00:40 2014 -0400
@@ -0,0 +1,97 @@
+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)