Mercurial > repos > lgueguen > sartools

comparison abims_sartools_deseq2_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
31 parser.add_argument('--alpha') 31 parser.add_argument('--alpha')
32 parser.add_argument('--pAdjustMethod') 32 parser.add_argument('--pAdjustMethod')
33 parser.add_argument('--typeTrans') 33 parser.add_argument('--typeTrans')
34 parser.add_argument('--locfunc') 34 parser.add_argument('--locfunc')
35 parser.add_argument('--colors') 35 parser.add_argument('--colors')
36 parser.add_argument('--forceCairoGraph')
36 parser.add_argument('--figures_html') 37 parser.add_argument('--figures_html')
37 parser.add_argument('--figures_html_files_path') 38 parser.add_argument('--figures_html_files_path')
38 parser.add_argument('--tables_html') 39 parser.add_argument('--tables_html')
39 parser.add_argument('--tables_html_files_path') 40 parser.add_argument('--tables_html_files_path')
40 parser.add_argument('--rdata') 41 parser.add_argument('--rdata')
55 alpha=args.alpha 56 alpha=args.alpha
56 pAdjustMethod=args.pAdjustMethod 57 pAdjustMethod=args.pAdjustMethod
57 typeTrans=args.typeTrans 58 typeTrans=args.typeTrans
58 locfunc=args.locfunc 59 locfunc=args.locfunc
59 colors=args.colors 60 colors=args.colors
61 forceCairoGraph=args.forceCairoGraph
60 figures_html=args.figures_html 62 figures_html=args.figures_html
61 figures_html_files_path=args.figures_html_files_path 63 figures_html_files_path=args.figures_html_files_path
62 tables_html=args.tables_html 64 tables_html=args.tables_html
63 tables_html_files_path=args.tables_html_files_path 65 tables_html_files_path=args.tables_html_files_path
64 rdata=args.rdata 66 rdata=args.rdata
97 cmd+="--typeTrans %s " % (typeTrans) 99 cmd+="--typeTrans %s " % (typeTrans)
98 if locfunc: 100 if locfunc:
99 cmd+="--locfunc %s " % (locfunc) 101 cmd+="--locfunc %s " % (locfunc)
100 if colors: 102 if colors:
101 cmd+="--colors %s " % (colors) 103 cmd+="--colors %s " % (colors)
104 if forceCairoGraph:
105 cmd+="--forceCairoGraph %s " % (forceCairoGraph)
102 cmd+="> %s 2>&1" % (log) 106 cmd+="> %s 2>&1" % (log)
103 print("Rscript command: %s") % (cmd) 107 print("Rscript command: %s") % (cmd)
104 os.system(cmd) 108 os.system(cmd)
105 109
106 #Get output files 110 #Get output files