Mercurial > repos > trinity_ctat > analyze_differential_expression

comparison analyze_diff_exp_wrapper.py @ 4:08f897c2b57e draft

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Adding some debugging statements.
author trinity_ctat
date Mon, 02 Oct 2017 13:53:09 -0400
parents b5d906ce0f06
children dab3b085f23d
comparison
equal deleted inserted replaced
3:b5d906ce0f06 4:08f897c2b57e
78 sys.stderr.write(cmd_stderr) 78 sys.stderr.write(cmd_stderr)
79 return 79 return
80 80
81 print "" 81 print ""
82 Final_tar_gz= "edgeR.tar.gz" 82 Final_tar_gz= "edgeR.tar.gz"
83 run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz") 83 run_command("cp "+ sys.argv[1] + " " + Final_tar_gz)
84 run_command("tar -xvf " + "Final_tar_gz") 84 run_command("tar -xzvf " + Final_tar_gz)
85 run_command("mv " + "edgeR_results" + "/* ." ) 85 run_command("mv " + "edgeR_results" + "/* ." )
86 86
87 print "" 87 print ""
88 run_command("pwd") 88 run_command("pwd")
89 run_command("ls -lad ./*") 89 run_command("ls -lad ./*")
90 print "\nedgeR_results" 90 print "\nedgeR_results/"
91 run_command("ls -lad edgeR_results/*") 91 run_command("ls -la edgeR_results")
92 92
93 # run the analyze command 93 # run the analyze command
94 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue 94 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue
95 run_command(cmd) 95 run_command(cmd)
96 96