Mercurial > repos > trinity_ctat > analyze_differential_expression
changeset 2:6f54e220d035 draft
Adding some debugging statements.
| author | trinity_ctat |
|---|---|
| date | Mon, 02 Oct 2017 12:55:27 -0400 |
| parents | 54f173578868 |
| children | b5d906ce0f06 |
| files | analyze_diff_exp_wrapper.py |
| diffstat | 1 files changed, 17 insertions(+), 11 deletions(-) [+] |
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--- a/analyze_diff_exp_wrapper.py Mon Oct 02 11:53:20 2017 -0400 +++ b/analyze_diff_exp_wrapper.py Mon Oct 02 12:55:27 2017 -0400 @@ -56,23 +56,29 @@ Cvalue=sys.argv[4] def run_command(cmd): - print "The command used: " + cmd - pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE) - pipe.wait() - ret= pipe.returncode - if ret: - print "command died: " + str(ret) - print pipe.stderr.readlines() - sys.exit(1) - else: - return -print " " + print "The command used: " + cmd + pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE) + pipe.wait() + ret= pipe.returncode + if ret: + print "command died: " + str(ret) + print pipe.stderr.readlines() + sys.exit(ret) + else: + return +print "" Final_tar_gz= "edgeR.tar.gz" run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz") run_command("tar -xvf " + "Final_tar_gz") run_command("mv " + "edgeR_results" + "/* ." ) +print "" +run_command("pwd") +run_command("ls -lad ./*") +print "\nedgeR_results" +run_command("ls -lad edgeR_results/*") + # run the analyze command cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue run_command(cmd)