Mercurial > repos > trinity_ctat > analyze_differential_expression

comparison analyze_diff_exp_wrapper.py @ 2:6f54e220d035 draft

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Adding some debugging statements.
author trinity_ctat
date Mon, 02 Oct 2017 12:55:27 -0400
parents 5bbc80dbfb5f
children b5d906ce0f06
comparison
equal deleted inserted replaced
1:54f173578868 2:6f54e220d035
54 Normalized_Matrix=sys.argv[2] 54 Normalized_Matrix=sys.argv[2]
55 Pvalue=sys.argv[3] 55 Pvalue=sys.argv[3]
56 Cvalue=sys.argv[4] 56 Cvalue=sys.argv[4]
57 57
58 def run_command(cmd): 58 def run_command(cmd):
59 print "The command used: " + cmd 59 print "The command used: " + cmd
60 pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE) 60 pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
61 pipe.wait() 61 pipe.wait()
62 ret= pipe.returncode 62 ret= pipe.returncode
63 if ret: 63 if ret:
64 print "command died: " + str(ret) 64 print "command died: " + str(ret)
65 print pipe.stderr.readlines() 65 print pipe.stderr.readlines()
66 sys.exit(1) 66 sys.exit(ret)
67 else: 67 else:
68 return 68 return
69 print " "
70 69
70 print ""
71 Final_tar_gz= "edgeR.tar.gz" 71 Final_tar_gz= "edgeR.tar.gz"
72 run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz") 72 run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz")
73 run_command("tar -xvf " + "Final_tar_gz") 73 run_command("tar -xvf " + "Final_tar_gz")
74 run_command("mv " + "edgeR_results" + "/* ." ) 74 run_command("mv " + "edgeR_results" + "/* ." )
75
76 print ""
77 run_command("pwd")
78 run_command("ls -lad ./*")
79 print "\nedgeR_results"
80 run_command("ls -lad edgeR_results/*")
75 81
76 # run the analyze command 82 # run the analyze command
77 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue 83 cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue
78 run_command(cmd) 84 run_command(cmd)
79 85