--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/effectiveT3/effectiveT3.py	Thu May 16 04:45:41 2013 -0400
@@ -0,0 +1,151 @@
+#!/usr/bin/env python
+"""Wrapper for EffectiveT3 v1.0.1 for use in Galaxy.
+
+This script takes exactly five command line arguments:
+ * model name (e.g. TTSS_STD-1.0.1.jar)
+ * threshold (selective or sensitive)
+ * an input protein FASTA filename
+ * output tabular filename
+
+It then calls the standalone Effective T3 v1.0.1 program (not the
+webservice), and reformats the semi-colon separated output into
+tab separated output for use in Galaxy.
+"""
+import sys
+import os
+import subprocess
+
+#The Galaxy auto-install via tool_dependencies.xml will set this environment variable
+effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
+effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar")
+
+if "-v" in sys.argv or "--version" in sys.argv:
+    #TODO - Get version of the JAR file dynamically?
+    print "Wrapper v0.0.11, TTSS_GUI-1.0.1.jar"
+    sys.exit(0)
+
+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) != 5:
+   stop_err("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
+
+model, threshold, fasta_file, tabular_file = sys.argv[1:]
+
+if not os.path.isfile(fasta_file):
+   stop_err("Input FASTA file not found: %s" % fasta_file)
+
+if threshold not in ["selective", "sensitive"] \
+and not threshold.startswith("cutoff="):
+   stop_err("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
+
+def clean_tabular(raw_handle, out_handle):
+    """Clean up Effective T3 output to make it tabular."""
+    count = 0
+    positive = 0
+    errors = 0
+    for line in raw_handle:
+        if not line or line.startswith("#") \
+        or line.startswith("Id; Description; Score;"):
+            continue
+        assert line.count(";") >= 3, repr(line)
+        #Normally there will just be three semi-colons, however the
+        #original FASTA file's ID or description might have had
+        #semi-colons in it as well, hence the following hackery:
+        try:
+            id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2)
+            #Cope when there was no FASTA description
+            if "; " not in id_descr and id_descr.endswith(";"):
+                id = id_descr[:-1]
+                descr = ""
+            else:
+                id, descr = id_descr.split("; ",1)
+        except ValueError:
+            stop_err("Problem parsing line:\n%s\n" % line)
+        parts = [s.strip() for s in [id, descr, score, effective]]
+        out_handle.write("\t".join(parts) + "\n")
+        count += 1
+        if float(score) < 0:
+           errors += 1
+        if effective.lower() == "true":
+           positive += 1
+    return count, positive, errors
+
+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))
+
+if not os.path.isdir(effectiveT3_dir):
+    stop_err("Effective T3 folder not found: %r" % effectiveT3_dir)
+
+if not os.path.isfile(effectiveT3_jar):
+    stop_err("Effective T3 JAR file not found: %r" % effectiveT3_jar)
+
+if not os.path.isdir(os.path.join(effectiveT3_dir, "module")):
+    stop_err("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module"))
+
+effectiveT3_model = os.path.join(effectiveT3_dir, "module", model)
+if not os.path.isfile(effectiveT3_model):
+    sys.stderr.write("Contents of %r is %s\n"
+                     % (os.path.join(effectiveT3_dir, "module"),
+                        ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module")))))
+    sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar)
+    stop_err("Effective T3 model JAR file not found: %r" % effectiveT3_model)
+
+#We will have write access whereever the output should be,
+temp_file = os.path.abspath(tabular_file + ".tmp")
+
+#Use absolute paths since will change current directory...
+tabular_file = os.path.abspath(tabular_file)
+fasta_file = os.path.abspath(fasta_file)
+
+cmd = ["java", "-jar", effectiveT3_jar,
+       "-f", fasta_file,
+       "-m", model,
+       "-t", threshold,
+       "-o", temp_file,
+       "-q"]
+
+try:
+    #Must run from directory above the module subfolder:
+    os.chdir(effectiveT3_dir)
+except:
+    stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir)
+
+run(cmd)
+
+if not os.path.isfile(temp_file):
+   stop_err("ERROR - No output file from Effective T3")
+
+out_handle = open(tabular_file, "w")
+out_handle.write("#ID\tDescription\tScore\tEffective\n")
+data_handle = open(temp_file)
+count, positive, errors = clean_tabular(data_handle, out_handle)
+data_handle.close()
+out_handle.close()
+
+os.remove(temp_file)
+
+if errors:
+   print "%i sequences, %i positive, %i errors" \
+         % (count, positive, errors)
+else:
+   print "%i/%i sequences positive" % (positive, count)
+
+if count and count==errors:
+   #Galaxy will still  allow them to see the output file
+   stop_err("All your sequences gave an error code")