diff ctat_trinity_tool_wrapper.py @ 0:5eca0c75b178 draft default tip

Upload ctat tools.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_trinity_tool_wrapper.py	Tue Jul 17 11:47:32 2018 -0400
@@ -0,0 +1,123 @@
+#!/usr/bin/env python
+
+
+# borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools.
+
+"""
+Wrapper that execute a program and its arguments but reports standard error
+messages only if the program exit status was not 0
+Example: ./stderr_wrapper.py myprog arg1 -f arg2
+"""
+
+import sys, subprocess, os
+print sys.version
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+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.
+    # 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 just 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)
+
+
+# get bindir
+bindir = sys.argv[0]
+bindir = bindir.split("/")
+if len(bindir) > 1:
+    bindir.pop()
+    bindir = "/".join(bindir)
+else:
+    bindir = "."
+
+
+## add locations of tools to path setting.
+#TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt";
+#for line in open(TOOL_PATHS_FILE):
+#    line = line.rstrip()
+#    os.environ['PATH'] += ":" + line
+
+# Add TrinityPath and its utils to the PATH environment variable.
+# print "Initially the PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
+os.environ['PATH'] = os.environ['PATH'] + ":{:s}:{:s}".format(TRINITY_BASE_DIR,TRINITY_BASE_DIR+"/util")
+# print "Now the PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
+
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def __main__():
+    # Get command-line arguments
+    args = sys.argv
+    # Remove name of calling program, i.e. ./stderr_wrapper.py
+    args.pop(0)
+    # If there are no arguments left, we're done
+    if len(args) == 0:
+        return
+
+    # If one needs to silence stdout 
+    #args.append( ">" )
+    #args.append( "/dev/null" )
+    print "The TRINITY_BASE_DIR is:\n\t{:s}".format(TRINITY_BASE_DIR)
+    print "The PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
+
+    args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]);
+
+    cmdline = " ".join(args)
+
+    print "The command being invoked is:\n\t{:s}".format(cmdline)
+    
+
+    try:
+        # Run program
+        err_capture = open("stderr.txt", 'w')
+        proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout )
+        returncode = proc.wait()
+        err_capture.close()
+
+        
+        if returncode != 0:
+            raise Exception
+
+    except Exception:
+        # Running Grinder failed: write error message to stderr
+        err_text = open("stderr.txt").readlines()
+        stop_err( "ERROR:\n" + "\n".join(err_text))
+
+
+if __name__ == "__main__": __main__()