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Updated the structure of the libraries
author george.weingart@gmail.com
date Mon, 09 Feb 2015 12:17:40 -0500
parents e0b5980139d9
children
comparison
equal deleted inserted replaced
7:c72e14eabb08 8:e9677425c6c3
1 import sfle
2 import csv
3
4 Import( "*" )
5 pE = DefaultEnvironment( )
6
7 # Extensions
8 sGraphlanAnnotationFileExtension = "-ann.txt"
9 sGraphlanCoreAnnotFileExtension = "-ann-core.txt"
10 sGraphlanCoreGenesFileExtension = "-core.txt"
11 sGraphlanFigureExtension = "-graphlan.pdf"
12 sMaaslinDataFileExtension = ".txt"
13 sMaaslinReadConfigFileExtension = ".read.config"
14 sMaaslinSummaryFileExtension = ".txt"
15
16 sCustomRScriptExtension = ".R"
17 sPCLExtension = ".pcl"
18 sTransposeExtension = ".tsv"
19
20 # Files
21 strMaaslinGraphlanSettings = "Graphlan_settings.txt"
22
23 # Script
24 sScriptGraphlan = File(os.path.join("..","graphlan","graphlan.py"))
25 sScriptGraphlanAnnotate = File(os.path.join("..","graphlan","graphlan_annotate.py"))
26 sScriptMaaslinSummaryToGraphlanAnnotation = File(sfle.d(fileDirSrc,"MaaslinToGraphlanAnnotation.py"))
27 sScriptPCLToCoreGene = File(sfle.d(fileDirSrc,"PCLToGraphlanCoreGene.py"))
28
29 sProgMaaslin = sfle.d(fileDirSrc,"Maaslin.R")
30
31 # Settings
32 iGraphlanDPI = 150
33 iGraphlanFigureSize = 4
34 iGraphlanPad = 0.2
35 strGraphlanDirectory = "graphlan"
36
37 c_fileDirLib = sfle.d( fileDirSrc, "lib" )
38 c_fileInputMaaslinR = sfle.d( pE, fileDirSrc, "Maaslin.R" )
39 c_afileTestsR = [sfle.d( pE, c_fileDirLib, s ) for s in
40 ("IO.R", "SummarizeMaaslin.R", "Utility.R", "ValidateData.R")]
41
42 c_afileDocsR = c_afileTestsR + [sfle.d( pE, c_fileDirLib, s ) for s in
43 ( "AnalysisModules.R", "scriptBiplotTSV.R", "BoostGLM.R", "Constants.R", "MaaslinPlots.R")]
44
45 ##Test scripts
46 for fileInputR in c_afileTestsR:
47 strBase = sfle.rebase( fileInputR, True )
48 #Testing summary file
49 fileTestingSummary = sfle.d( pE, fileDirOutput, strBase +"-TestReport.txt" )
50 dirTestingR = Dir( sfle.d( fileDirSrc, "test-" + strBase ) )
51 Default( sfle.testthat( pE, fileInputR, dirTestingR, fileTestingSummary ) )
52
53 ##Inline doc
54 for fileProg in c_afileDocsR:
55 filePDF = sfle.d( pE, fileDirOutput, sfle.rebase( fileProg, sfle.c_strSufR, sfle.c_strSufPDF ) )
56 Default( sfle.inlinedocs( pE, fileProg, filePDF, fileDirTmp ) )
57
58 ##Start regression suite
59 execfile( "SConscript_maaslin.py" )
60
61 ##Input pcl files
62 lsMaaslinInputFiles = Glob( sfle.d( fileDirInput, "*" + sfle.c_strSufPCL ) )
63
64 ## Run MaAsLin and generate output
65 for strPCLFile in lsMaaslinInputFiles:
66 Default( MaAsLin( strPCLFile ))
67
68 # #Graphlan figure
69 # #TODO Fix path dependent, better way to know it is installed?
70 # if(os.path.exists(sScriptGraphlan.get_abspath())):
71
72 # ## Run Graphlan on all output projects
73 # strProjectName = os.path.splitext(os.path.split(strPCLFile.get_abspath())[1])[0]
74 # strMaaslinOutputDir = sfle.d(fileDirOutput,strProjectName)
75
76 # ##Get maaslin data files
77 # strMaaslinSummaryFile = sfle.d(os.path.join(strMaaslinOutputDir, strProjectName + sMaaslinSummaryFileExtension))
78
79 # # Make core gene file
80 # sCoreGeneFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanCoreGenesFileExtension))))
81 # sReadConfigFile = File(sfle.d(fileDirInput,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sMaaslinReadConfigFileExtension)))
82 # sfle.op(pE, sScriptPCLToCoreGene, [[False, strPCLFile],[False, sReadConfigFile],[True, sCoreGeneFile]])
83
84 # # Make annotation file
85 # sAnnotationFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanAnnotationFileExtension))))
86 # sfle.op(pE, sScriptMaaslinSummaryToGraphlanAnnotation, [[False, strMaaslinSummaryFile],[False,sCoreGeneFile],[False,File(sfle.d(fileDirSrc,strMaaslinGraphlanSettings))],[True,sAnnotationFile]])
87
88 # # Generate core gene annotation file names
89 # sCoreGeneAnnotationFile = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory,sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanCoreAnnotFileExtension))))
90 # sfle.op(pE, sScriptGraphlanAnnotate, ["--annot",[sAnnotationFile],[False, sCoreGeneFile],[True, sCoreGeneAnnotationFile]])
91
92 # # Call graphlan
93 # # graphlan.py --dpi 150 --size 4 --pad 0.2 core_genes.annot.xml core_genes.png
94 # sGraphlanFigure = File(sfle.d(strMaaslinOutputDir, os.path.join(strGraphlanDirectory, sfle.rebase(strMaaslinSummaryFile, sMaaslinSummaryFileExtension,sGraphlanFigureExtension))))
95 # sfle.op(pE, sScriptGraphlan, [[False, sCoreGeneAnnotationFile],[True, sGraphlanFigure],"--dpi",iGraphlanDPI,"--size",iGraphlanFigureSize,"--pad",iGraphlanPad])
96
97 # Default(sCoreGeneFile,sAnnotationFile,sCoreGeneAnnotationFile,sGraphlanFigure)