Mercurial > repos > lgueguen > sartools

comparison abims_sartools_edger_wrapper.py @ 3:de6d0b7c17af draft

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release 1.6.3
author lgueguen
date Mon, 01 Oct 2018 05:07:56 -0400
parents 581d217c7337
children 05c9b1a7f44e
comparison
equal deleted inserted replaced
2:d86ccac2a660 3:de6d0b7c17af
29 parser.add_argument('--pAdjustMethod') 29 parser.add_argument('--pAdjustMethod')
30 parser.add_argument('--cpmCutoff') 30 parser.add_argument('--cpmCutoff')
31 parser.add_argument('--geneSelection') 31 parser.add_argument('--geneSelection')
32 parser.add_argument('--normalizationMethod') 32 parser.add_argument('--normalizationMethod')
33 parser.add_argument('--colors') 33 parser.add_argument('--colors')
34 parser.add_argument('--forceCairoGraph')
34 parser.add_argument('--figures_html') 35 parser.add_argument('--figures_html')
35 parser.add_argument('--figures_html_files_path') 36 parser.add_argument('--figures_html_files_path')
36 parser.add_argument('--tables_html') 37 parser.add_argument('--tables_html')
37 parser.add_argument('--tables_html_files_path') 38 parser.add_argument('--tables_html_files_path')
38 parser.add_argument('--rdata') 39 parser.add_argument('--rdata')
51 pAdjustMethod=args.pAdjustMethod 52 pAdjustMethod=args.pAdjustMethod
52 cpmCutoff=args.cpmCutoff 53 cpmCutoff=args.cpmCutoff
53 geneSelection=args.geneSelection 54 geneSelection=args.geneSelection
54 normalizationMethod=args.normalizationMethod 55 normalizationMethod=args.normalizationMethod
55 colors=args.colors 56 colors=args.colors
57 forceCairoGraph=args.forceCairoGraph
56 figures_html=args.figures_html 58 figures_html=args.figures_html
57 figures_html_files_path=args.figures_html_files_path 59 figures_html_files_path=args.figures_html_files_path
58 tables_html=args.tables_html 60 tables_html=args.tables_html
59 tables_html_files_path=args.tables_html_files_path 61 tables_html_files_path=args.tables_html_files_path
60 rdata=args.rdata 62 rdata=args.rdata
89 cmd+="--gene.selection %s " % (geneSelection) 91 cmd+="--gene.selection %s " % (geneSelection)
90 if normalizationMethod: 92 if normalizationMethod:
91 cmd+="--normalizationMethod %s " % (normalizationMethod) 93 cmd+="--normalizationMethod %s " % (normalizationMethod)
92 if colors: 94 if colors:
93 cmd+="--colors %s " % (colors) 95 cmd+="--colors %s " % (colors)
96 if forceCairoGraph:
97 cmd+="--forceCairoGraph %s " % (forceCairoGraph)
94 cmd+="> %s 2>&1" % (log) 98 cmd+="> %s 2>&1" % (log)
95 print("Rscript command: %s") % (cmd) 99 print("Rscript command: %s") % (cmd)
96 os.system(cmd) 100 os.system(cmd)
97 101
98 #Get output files 102 #Get output files