view maaslin-4450aa4ecc84/SConscript @ 2:589169d452c0

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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)