Mercurial > repos > lgueguen > sartools

comparison abims_sartools_deseq2_wrapper.py @ 4:05c9b1a7f44e draft default tip

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Uploaded new release 1.7.3
author lgueguen
date Thu, 07 Jan 2021 11:12:01 +0000
parents de6d0b7c17af
children
comparison
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3:de6d0b7c17af 4:05c9b1a7f44e
65 tables_html_files_path=args.tables_html_files_path 65 tables_html_files_path=args.tables_html_files_path
66 rdata=args.rdata 66 rdata=args.rdata
67 report_html=args.report_html 67 report_html=args.report_html
68 log=args.log 68 log=args.log
69 #Print the parameters selected 69 #Print the parameters selected
70 print("Wrapper arguments: %s") %(args) 70 print("Wrapper arguments: %s" %(args))
71 71
72 #Get the working directory path 72 #Get the working directory path
73 working_directory = os.getcwd() 73 working_directory = os.getcwd()
74 #Get the script directory path 74 #Get the script directory path
75 script_directory=os.path.dirname(os.path.realpath(__file__)) 75 script_directory=os.path.dirname(os.path.realpath(__file__))
102 if colors: 102 if colors:
103 cmd+="--colors %s " % (colors) 103 cmd+="--colors %s " % (colors)
104 if forceCairoGraph: 104 if forceCairoGraph:
105 cmd+="--forceCairoGraph %s " % (forceCairoGraph) 105 cmd+="--forceCairoGraph %s " % (forceCairoGraph)
106 cmd+="> %s 2>&1" % (log) 106 cmd+="> %s 2>&1" % (log)
107 print("Rscript command: %s") % (cmd) 107 print("Rscript command: %s" % (cmd))
108 os.system(cmd) 108 os.system(cmd)
109 109
110 #Get output files 110 #Get output files
111 os.mkdir(figures_html_files_path) 111 os.mkdir(figures_html_files_path)
112 os.mkdir(tables_html_files_path) 112 os.mkdir(tables_html_files_path)