--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/LaunchMatcher.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,168 @@
+#!/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.LoggerFactory import LoggerFactory
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+import subprocess
+
+LOG_DEPTH = "repet.tools"
+
+##Launch MATCHER
+#
+class LaunchMatcher(object):
+
+    def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", doClean = False, verbosity = 0):
+        self._alignFileName = align
+        self._queryFileName = queryFileName
+        self.setSubjectFileName(subjectFileName)
+        self.setOutPrefix(prefix)
+        self._doJoin = doJoin
+        self._eValue = evalue
+        self._keepConflict = keepConflict
+        
+        self._doClean = doClean
+        self._verbosity = verbosity
+        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
+        
+    def setAttributesFromCmdLine(self):
+        description = "Launch Matcher."
+        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
+        epilog += "\t$ python LaunchMatcher.py -a in.align -v 0"
+        epilog += "\n\t"
+        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
+        epilog += "\t$ python LaunchMatcher.py -a in.align -q query.fa -s nr.fa -c -v 2"
+        parser = RepetOptionParser(description = description, epilog = epilog)
+        parser.add_option("-a", "--align",      dest = "align",         action = "store",       type = "string", help = "input align file name [compulsory] [format: align]",       default = "")
+        parser.add_option("-q", "--query",      dest = "query",         action = "store",       type = "string", help = "query fasta file name [optional] [format: fasta]",         default = "")
+        parser.add_option("-s", "--subject",    dest = "subject",       action = "store",       type = "string", help = "subject fasta file name [optional] [format: fasta]",       default = "")
+        parser.add_option("-e", "--evalue",     dest = "evalue",        action = "store",       type = "string", help = "E-value filter [default: 1e-10]",                          default = "1e-10")
+        parser.add_option("-j", "--join",       dest = "doJoin",        action = "store_true",                   help = "join matches [default: False]",                            default = False)
+        parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true",                   help = "keep conflicting subjects [default: False]",               default = False)
+        parser.add_option("-o", "--outPrefix",  dest = "outPrefix",     action = "store",       type = "string", help = "output file prefix [default: align file name]",            default = "")
+        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [default: False]",                   default = False)
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [default: 1]",                                   default = 1)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+        
+    def _setAttributesFromOptions(self, options):
+        self.setAlignFileName(options.align)
+        self.setQueryFileName(options.query)
+        self.setSubjectFileName(options.subject)
+        self.setEvalue(options.evalue)
+        self.setDoJoin(options.doJoin)
+        self.setKeepConflicts(options.keepConflict)
+        self.setOutPrefix(options.outPrefix)
+        self.setDoClean(options.doClean)
+        self.setVerbosity(options.verbosity)
+        
+    def setAlignFileName(self, alignFileName):
+        self._alignFileName = alignFileName
+        
+    def setQueryFileName(self, queryFileName):
+        self._queryFileName = queryFileName
+        
+    def setSubjectFileName(self, subjectFileName):
+        self._subjectFileName = subjectFileName
+        
+    def setEvalue(self, evalue):
+        self._eValue = evalue
+        
+    def setDoJoin(self, doJoin):
+        self._doJoin = doJoin
+        
+    def setKeepConflicts(self, keepConflict):
+        self._keepConflict = keepConflict
+        
+    def setOutPrefix(self, outPrefix):
+        if outPrefix == "":
+            self._outPrefix = self._alignFileName
+        else:
+            self._outPrefix = outPrefix
+        
+    def setDoClean(self, doClean):
+        self._doClean = doClean
+        
+    def setVerbosity(self, verbosity):
+        self._verbosity = verbosity
+        
+    def _checkOptions(self):
+        if self._alignFileName == "":
+            self._logAndRaise("ERROR: Missing input align file name")
+        
+    def _logAndRaise(self, errorMsg):
+        self._log.error(errorMsg)
+        raise Exception(errorMsg)
+
+    def _getMatcherCmd(self):
+        lArgs = []
+        lArgs.append("-m %s" % self._alignFileName)
+        if self._queryFileName:
+            lArgs.append("-q %s" % self._queryFileName)
+        if self._subjectFileName:
+            lArgs.append("-s %s" % self._subjectFileName)
+        if self._doJoin:
+            lArgs.append("-j")
+        lArgs.append("-E %s" % self._eValue)
+        lArgs.append("-B %s" % self._outPrefix)
+        if self._keepConflict:
+            lArgs.append("-a")
+        lArgs.append("-v %i" % (self._verbosity - 1))
+        return self._getSystemCommand("matcher", lArgs)
+    
+    def _getSystemCommand(self, prg, lArgs):
+        systemCmd = prg 
+        for arg in lArgs:
+            systemCmd += " " + arg
+        return systemCmd
+                    
+    def run(self):
+        LoggerFactory.setLevel(self._log, self._verbosity)
+        self._checkOptions()
+        self._log.info("START LaunchMatcher")
+        self._log.debug("Align file name: %s" % self._alignFileName)
+        self._log.debug("Query file name: %s" % self._queryFileName)
+        self._log.debug("Subject file name: %s" % self._subjectFileName)
+        #TODO: clean files
+#        if self._doClean:
+#            self._log.warning("Files will be cleaned")
+        cmd = self._getMatcherCmd()
+        process = subprocess.Popen(cmd, shell = True)
+        self._log.debug("Running : %s" % cmd)
+        process.communicate()
+        if process.returncode != 0:
+            self._logAndRaise("ERROR when launching '%s'" % cmd)
+        self._log.info("END LaunchMatcher")
+
+if __name__ == "__main__":
+    iLaunch = LaunchMatcher()
+    iLaunch.setAttributesFromCmdLine()
+    iLaunch.run()        
\ No newline at end of file