--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/blast2go.py	Tue Jun 07 16:28:31 2011 -0400
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+"""Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.3.5.
+
+This script takes exactly three command line arguments:
+ * Input BLAST XML filename
+ * Blast2GO properties filename (settings file)
+ * Output tabular filename
+
+It then calls the Java command line tool, and moves the output file to
+the location Galaxy is expecting.
+"""
+import sys
+import os
+import subprocess
+
+#You may need to edit this to match your local setup,
+blast2go_jar = "/opt/b2g4pipe/blast2go.jar"
+
+
+def stop_err(msg, error_level=1):
+   """Print error message to stdout and quit with given error level."""
+   sys.stderr.write("%s\n" % msg)
+   sys.exit(error_level)
+
+if len(sys.argv) != 4:
+   stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
+
+xml_file, prop_file, tabular_file = sys.argv[1:]
+
+if not os.path.isfile(xml_file):
+   stop_err("Input BLAST XML file not found: %s" % xml_file)
+
+if not os.path.isfile(prop_file):
+   stop_err("Blast2GO configuration file not found: %s" % prop_file)
+
+def run(cmd):
+    #Avoid using shell=True when we call subprocess to ensure if the Python
+    #script is killed, so too is the child process.
+    try:
+        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except Exception, err:
+        stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+    #Use .communicate as can get deadlocks with .wait(),
+    stdout, stderr = child.communicate()
+    return_code = child.returncode
+    if return_code:
+        if stderr and stdout:
+            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr))
+        else:
+            stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr))
+    #For early diagnostics,
+    else:
+       print stdout
+       print stderr
+
+if not os.path.isfile(blast2go_jar):
+   stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
+
+#We will have write access whereever the output should be,
+#so we'll ask Blast2GO to use that as the stem for its output
+#(it will append .annot to the filename)
+cmd = ["java", "-jar", blast2go_jar,
+       "-in", xml_file,
+       "-prop", prop_file,
+       "-out", tabular_file,
+       "-a"]
+run(cmd)
+
+out_file = tabular_file + ".annot"
+if not os.path.isfile(out_file):
+   stop_err("ERROR - No output annotation file from Blast2GO")
+
+#Move the output file where Galaxy expects it to be:
+os.rename(out_file, tabular_file)
+
+print "Done"