Mercurial > repos > trinity_ctat > analyze_differential_expression
changeset 5:dab3b085f23d draft
Adding more debugging statements.
| author | trinity_ctat |
|---|---|
| date | Mon, 02 Oct 2017 14:39:03 -0400 |
| parents | 08f897c2b57e |
| children | 9b2226f8c2fe |
| files | analyze_diff_exp_wrapper.py |
| diffstat | 1 files changed, 14 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/analyze_diff_exp_wrapper.py Mon Oct 02 13:53:09 2017 -0400 +++ b/analyze_diff_exp_wrapper.py Mon Oct 02 14:39:03 2017 -0400 @@ -59,6 +59,7 @@ # 2017-10-02 # Cicada Dennis put the subprocess command in a try/except statement. # Errors were going undetected the way it was written previously. + print "Running command:\n\t" + cmd try: pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE) cmd_stdout, cmd_stderr = pipe.communicate() @@ -74,21 +75,30 @@ sys.stderr.write(cmd_stderr) sys.exit(ret) else: - # Any error output written to stdout instead of stderr, since no error has occurred. + # Any error output is written to stdout instead of stderr, since no error has occurred. sys.stderr.write(cmd_stderr) return print "" Final_tar_gz= "edgeR.tar.gz" run_command("cp "+ sys.argv[1] + " " + Final_tar_gz) -run_command("tar -xzvf " + Final_tar_gz) -run_command("mv " + "edgeR_results" + "/* ." ) +run_command("tar -xvf " + Final_tar_gz) -print "" +print "Before moving files." run_command("pwd") run_command("ls -lad ./*") print "\nedgeR_results/" run_command("ls -la edgeR_results") +print "" + +run_command("mv edgeR_results /* ." ) + +print "After moving files." +run_command("pwd") +run_command("ls -lad ./*") +print "\nedgeR_results/" +run_command("ls -la edgeR_results") +print "" # run the analyze command cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " + Normalized_Matrix + " -P " + Pvalue + " -C " + Cvalue