--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/LaunchLastZ.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,133 @@
+#! /usr/bin/env python
+
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+import sys
+import os
+import optparse
+from commons.core.checker.CheckerUtils import CheckerUtils
+from commons.core.utils.FileUtils import FileUtils
+from subprocess import Popen
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+import subprocess
+import tempfile
+  
+class LaunchLastZ(object):
+
+    def __init__(self,queryFileName="", refFileName ="", outputFileName=None,outputFileFormat="axt",noTransition=True, ambiguous=None, step=1,gfextend=False, chain=False, verbosity=1 ):
+        self.queryFileName = queryFileName
+        self.refFileName = refFileName
+        self.outputFileName = outputFileName
+        self.outputFileFormat = outputFileFormat
+        self.noTransition = noTransition
+        self.step = step
+        self.ambiguous = ambiguous
+        self.gfextend = gfextend
+        self.chain = chain
+        self.verbosity = verbosity
+        
+    def setAttributesFromCmdLine(self):
+        description = "LaunchLastZ runs the LastZ program ."    
+        parser = RepetOptionParser(description = description)
+        parser.add_option("-q", "--query", dest="queryFileName", default = None,  action="store", type="string", help="input query file [compulsory] [format: fasta]")
+        parser.add_option("-r", "--ref", dest="refFileName", default = None,  action="store", type="string", help="input ref file [compulsory] [format: fasta]")
+        parser.add_option("-o", "--output", dest="outputFileName", default = None,  action="store", type="string", help="output file [compulsory] ")
+        parser.add_option("-f", "--format", dest="outputFileFormat", default = "axt",  action="store", type="string", help="output file format[optional] ")
+        parser.add_option("-n", "--notransition", dest="noTransition", action="store_false", default=True, help="noTransition (default True) [optional] ")
+        parser.add_option("-a", "--ambiguous", dest="ambiguous", action="store",  type="string", help="ambiguous [optional] ")
+        parser.add_option("-s", "--step", dest="step", default = 1,  action="store", type="int", help="stepsize (default 1) [optional] ")
+        parser.add_option("-g", "--gfextend", dest="gfextend",  action="store_true",  help="extend gf (default false)[optional] ")
+        parser.add_option("-c", "--chain", dest="chain",  action="store_true", help="chain (default false)[optional] ")
+        parser.add_option("-v", "--verbosity", dest="verbosity", default = 1,  action="store", type="int", help="verbosity [optional] ")
+        (self._options, args) = parser.parse_args()
+        self._setAttributesFromOptions(self._options)
+
+    def _setAttributesFromOptions(self, options):
+        self.queryFileName = options.queryFileName
+        self.refFileName = options.refFileName
+        self.outputFileName = options.outputFileName
+        self.outputFileFormat = options.outputFileFormat
+	self.ambiguous = options.ambiguous
+        self.noTransition = options.noTransition
+        self.step = options.step
+        self.gfextend = options.gfextend
+        self.chain = options.chain
+        self.verbosity = options.verbosity
+      
+    def checkOptions(self):       
+        if self.queryFileName != "":
+            if not FileUtils.isRessourceExists(self.queryFileName):
+                raise Exception("ERROR: Query file does not exist!")
+        else:
+            raise Exception("ERROR: No specified --query option!")
+        if self.refFileName != "":
+            if not FileUtils.isRessourceExists(self.refFileName):
+                raise Exception("ERROR: Ref file does not exist!")
+        else:
+            raise Exception("ERROR: No specified --ref option!")
+        if self.outputFileName == None:
+            self.outputFileName = "%s_%s.axt" % (os.path.basename(self.queryFileName), os.path.basename(self.refFileName))
+                                
+    def run(self):
+        if not CheckerUtils.isExecutableInUserPath("lastz") :
+            print ("ERROR: LastZ must be in your path")
+        else:
+            self.checkOptions()
+            
+            transition = "" 
+            if self.noTransition:
+                transition = "--notransition"
+            ambiguous = ""    
+            if self.ambiguous is not None:
+                ambiguous =  "--ambiguous=%s" % self.ambiguous
+                
+            gfextend = ""
+            if self.gfextend:
+                gfextend = "--gfextend"
+                
+            chain = ""
+            if self.chain:
+                chain = "--chain"
+                
+            cmd = "lastz %s[format=fasta] %s[format=fasta] --output=%s --format=%s %s %s --step=%i %s %s" % (self.refFileName, self.queryFileName, self.outputFileName
+                                                                           , self.outputFileFormat, ambiguous, transition,self.step, gfextend, chain)
+            if self.verbosity>0:
+                print("Running LastZ with following commands : %s" %cmd)
+            sys.stdout.flush()
+            cmd = cmd.split()
+            process = subprocess.Popen(cmd)
+            process.wait()
+            return process.returncode
+
+if __name__ == "__main__":
+    iLaunchLastZ = LaunchLastZ()
+    iLaunchLastZ.setAttributesFromCmdLine()
+    iLaunchLastZ.run()