--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/LaunchMummerPlot.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,150 @@
+#! /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.
+
+from commons.core.checker.CheckerUtils import CheckerUtils
+from commons.core.utils.FileUtils import FileUtils
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+import subprocess
+from commons.core.LoggerFactory import LoggerFactory
+import os
+import shutil
+  
+LOG_DEPTH = "repet.tools"  
+  
+class LaunchMummerPlot(object):
+
+    def __init__(self, inputFileName="", queryFileName="", refFileName ="", prefix = None, fat=False, filter=False,clean=False, verbosity=0):
+        self._inputFileName = inputFileName
+        self._queryFileName = queryFileName
+        self._refFileName = refFileName
+        self._prefix = prefix
+        self._fat = fat
+        self._filter = filter
+        self.doClean = clean
+        self.verbosity = verbosity
+        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
+             
+    def setAttributesFromCmdLine(self):
+        description = "LaunchMummerPlot runs the MummerPlot program (part of the mummer package) ."    
+        parser = RepetOptionParser(description = description)
+        parser.add_option("-i", "--input", dest="inputFileName", default = None,  action="store", type="string", help="input file[mandatory] [format: delta]")      
+        parser.add_option("-q", "--Qfile", dest="queryFileName", default = None,  action="store", type="string", help="Plot an ordered set of reference sequences from Qfile [optional] [format: fasta]")
+        parser.add_option("-r", "--Rfile", dest="refFileName", default = None,  action="store", type="string", help="Plot an ordered set of reference sequences from Rfile [optional] [format: fasta]")
+        parser.add_option("-p", "--prefix", dest="prefix", default = None,  action="store", type="string", help="prefix name [mandatory]")
+        parser.add_option("-o","--fat", dest="fat",action="store_true", help="Layout sequences using fattest alignment only[optional] ")
+        parser.add_option("-s","--filter", dest="filter",action="store_true", help="Only display .delta alignments which represent the 'best' hit [optional] ")      
+        parser.add_option("-c", "--clean", dest = "clean", help = "clean temporary files", default = False, action="store_true")  
+        parser.add_option("-v", "--verbosity", dest="verbosity", default = 0,  action="store", type="int", help="verbosity [optional] ")
+        
+        (self._options, args) = parser.parse_args()
+        self._setAttributesFromOptions(self._options)
+
+    def _setAttributesFromOptions(self, options):
+        self._inputFileName = options.inputFileName
+        self._queryFileName = options.queryFileName
+        self._refFileName = options.refFileName
+        self._prefix = options.prefix
+        self._fat = options.fat
+        self._filter = options.filter
+        self.verbosity = options.verbosity
+        
+    def _logAndRaise(self, errorMsg):
+        self._log.error(errorMsg)
+        raise Exception(errorMsg)
+            
+    def checkOptions(self):  
+        if self._inputFileName != "":
+            if not FileUtils.isRessourceExists(self._inputFileName):
+                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._inputFileName)
+        else:
+            self._logAndRaise("ERROR: No specified --query option!")     
+        
+        if self._queryFileName != "":
+            if not FileUtils.isRessourceExists(self._queryFileName):
+                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName)
+        
+        if self._refFileName != "":
+            if not FileUtils.isRessourceExists(self._refFileName):
+                self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName)
+                
+    def clean(self):
+        try:
+            os.remove("%s.filter" % self._prefix)
+        except Exception as inst: 
+            self._log.error(inst)
+        try:
+            os.remove("%s.fplot" % self._prefix)
+        except Exception as inst: 
+            self._log.error(inst)
+        try:
+            os.remove("%s.rplot" % self._prefix)
+        except Exception as inst: 
+            self._log.error(inst)
+                                
+    def run(self):
+        if not CheckerUtils.isExecutableInUserPath("mummerplot") :
+            self._logAndRaise("ERROR: mummerplot must be in your path")
+        self.checkOptions()
+        
+        ref=""
+        if self._refFileName != "":
+            ref = "-R %s"  % self._refFileName
+           
+        query=""
+        if self._queryFileName != "":
+            query = "-Q %s"  % self._queryFileName
+           
+        fat = ""
+        if self._fat:
+            fat =  "--fat"
+            
+        filter = ""
+        if self._filter:
+            filter = "-f" 
+            
+        prefix = ""
+        if self._prefix is not None:
+            prefix = "--prefix=%s" %(self._prefix)
+            
+        cmd = "mummerplot %s %s %s %s %s %s --png" % (self._inputFileName, prefix, ref, query, fat, filter)
+        self._log.debug("Running mummerplot with following commands : %s" %cmd)
+        cmd = cmd.split()         
+        process = subprocess.Popen(cmd)
+        process.wait()
+        
+        self.clean()
+        return process.returncode
+            
+if __name__ == "__main__":
+    iLaunchNucmer = LaunchMummerPlot()
+    iLaunchNucmer.setAttributesFromCmdLine()
+    iLaunchNucmer.run()
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