# HG changeset patch
# User trinity_ctat
# Date 1523544518 14400
# Node ID 03155bc11cff17dee866f103a83883f212d339da
# Parent 6a8dadcd45e3f731f3683079d831d2b6d11be576
Making sure tools are up to date.
diff -r 6a8dadcd45e3 -r 03155bc11cff ctat_analyze_diff_exp_wrapper.py
--- a/ctat_analyze_diff_exp_wrapper.py Thu Apr 12 10:10:11 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-import sys, os, subprocess
-
-TRINITY_BASE_DIR = ""
-if os.environ.has_key('TRINITY_HOME'):
- TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
-elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python.
- # 2017-09-26
- # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
- # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
- # I also found distutils.spawn.find_executable() which might work, but already implemented the below.
- try:
- pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
- except:
- msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0])
- sys.stderr.write(msg)
- # t, v, tb = sys.exc_info()
- # raise t, v, tb
- # For some reason the above was giving a syntax error.
- # A simple raise should reraise the existing exception.
- raise
- else:
- TrinityPath, err_info = pipe1.communicate()
- # FIX - probably should be checking err_info for errors...
- # Determine the TRINITY_BASE_DIR from output1.
- # If TrinityPath is a link, we need to dereference the link.
- TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
- # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
- # print os.path.islink(TrinityPath)
- TrinityPath = os.path.abspath(TrinityPath)
- # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
- # print msg
- # print os.path.islink(TrinityPath)
- while os.path.islink(TrinityPath):
- # print "That path is a link."
- TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
- # print "The new path is: {:s}".format(TrinityPath)
- # Take off the last part of the path (which is the Trinity command)
- TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
-else:
- sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
- sys.exit(1)
-
-usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value"
-print sys.argv
-print usage
-print " "
-
-if len(sys.argv)<5:
- print "Require atleast two parameters"
-else:
- print "All good- command going ahead"
-print " "
-
-Normalized_Matrix=sys.argv[2]
-Pvalue=sys.argv[3]
-Cvalue=sys.argv[4]
-
-def run_command(cmd):
- # 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()
- except:
- msg = "ERROR while running command:\n\t" + cmd
- sys.stderr.write(msg)
- raise
-
- sys.stdout.write(cmd_stdout)
- ret = pipe.returncode
- if ret:
- print "command died: " + str(ret)
- sys.stderr.write(cmd_stderr)
- sys.exit(ret)
- else:
- # 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 -xvf " + Final_tar_gz)
-
-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
-run_command(cmd)
-
-origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix"
-# diffExpr.P0.001_C2.0.matrix
-run_command("mv " + origMatrixName + " diffExpr.matrix")
-
-SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor.dat"
-# diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat
-run_command("mv " + SampleCorName + " diffExpr.matrix.log2.sample_cor.dat")
-
-CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor_matrix.pdf"
-# diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf
-run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf")
-
-Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf"
-#diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf
-run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf")
-
-sys.exit(0)
diff -r 6a8dadcd45e3 -r 03155bc11cff ctat_analyze_differential_expression.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_analyze_differential_expression.py Thu Apr 12 10:48:38 2018 -0400
@@ -0,0 +1,123 @@
+import sys, os, subprocess
+
+TRINITY_BASE_DIR = ""
+if os.environ.has_key('TRINITY_HOME'):
+ TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
+elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python.
+ # 2017-09-26
+ # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
+ # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
+ # I also found distutils.spawn.find_executable() which might work, but already implemented the below.
+ try:
+ pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
+ except:
+ msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0])
+ sys.stderr.write(msg)
+ # t, v, tb = sys.exc_info()
+ # raise t, v, tb
+ # For some reason the above was giving a syntax error.
+ # A simple raise should reraise the existing exception.
+ raise
+ else:
+ TrinityPath, err_info = pipe1.communicate()
+ # FIX - probably should be checking err_info for errors...
+ # Determine the TRINITY_BASE_DIR from output1.
+ # If TrinityPath is a link, we need to dereference the link.
+ TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
+ # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
+ # print os.path.islink(TrinityPath)
+ TrinityPath = os.path.abspath(TrinityPath)
+ # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
+ # print msg
+ # print os.path.islink(TrinityPath)
+ while os.path.islink(TrinityPath):
+ # print "That path is a link."
+ TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
+ # print "The new path is: {:s}".format(TrinityPath)
+ # Take off the last part of the path (which is the Trinity command)
+ TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
+else:
+ sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
+ sys.exit(1)
+
+usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value"
+print sys.argv
+print usage
+print " "
+
+if len(sys.argv)<5:
+ print "Require atleast two parameters"
+else:
+ print "All good- command going ahead"
+print " "
+
+Normalized_Matrix=sys.argv[2]
+Pvalue=sys.argv[3]
+Cvalue=sys.argv[4]
+
+def run_command(cmd):
+ # 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()
+ except:
+ msg = "ERROR while running command:\n\t" + cmd
+ sys.stderr.write(msg)
+ raise
+
+ sys.stdout.write(cmd_stdout)
+ ret = pipe.returncode
+ if ret:
+ print "command died: " + str(ret)
+ sys.stderr.write(cmd_stderr)
+ sys.exit(ret)
+ else:
+ # 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 -xvf " + Final_tar_gz)
+
+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
+run_command(cmd)
+
+origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix"
+# diffExpr.P0.001_C2.0.matrix
+run_command("mv " + origMatrixName + " diffExpr.matrix")
+
+SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor.dat"
+# diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat
+run_command("mv " + SampleCorName + " diffExpr.matrix.log2.sample_cor.dat")
+
+CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor_matrix.pdf"
+# diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf
+run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf")
+
+Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf"
+#diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf
+run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf")
+
+sys.exit(0)
diff -r 6a8dadcd45e3 -r 03155bc11cff ctat_analyze_differential_expression.xml
--- a/ctat_analyze_differential_expression.xml Thu Apr 12 10:10:11 2018 -0400
+++ b/ctat_analyze_differential_expression.xml Thu Apr 12 10:48:38 2018 -0400
@@ -13,7 +13,7 @@