--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/LaunchTRF.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,155 @@
+#!/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
+from commons.core.checker.ConfigChecker import ConfigRules
+from commons.core.checker.ConfigChecker import ConfigChecker
+import subprocess
+import glob
+import os
+
+LOG_DEPTH = "repet.launchers"
+
+class LaunchTRF(object):
+    
+    def __init__(self, inFileName = "", outFileName = "", maxPeriod=15, doClean = False, verbosity = 0):
+        self.inFileName = inFileName
+        self.setOutFileName(outFileName)
+        self.maxPeriod=maxPeriod
+        self._doClean = doClean
+        self._verbosity = verbosity
+        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
+        
+    def setAttributesFromCmdLine(self):
+        description = "Launch TRF to detect micro-satellites in sequences."
+        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
+        epilog += "\t$ python LaunchTemplate.py -i file.fa -v 0"
+        epilog += "\n\t"
+        parser = RepetOptionParser(description = description, epilog = epilog)
+        parser.add_option("-i", "--in",      dest = "inFileName", action = "store",       type = "string", help = "input file name [compulsory] [format: fasta]", default = "")
+        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.TRF.set]", default = "")
+        parser.add_option("-m", "--maxPeriod",  dest = "maxPeriod",     action = "store",       type = "int",    help = " maximum period size to report  [default: 15]", default = 15)
+        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+        
+    def _setAttributesFromOptions(self, options):
+        self.setInFileName(options.inFileName)
+        self.setOutFileName(options.outFileName)
+        self.maxPeriod = options.maxPeriod
+        self.setDoClean(options.doClean)
+        self.setVerbosity(options.verbosity)
+                
+    def setInFileName(self, inFileName):
+        self.inFileName = inFileName
+        
+    def setOutFileName(self, outFileName):
+        if outFileName == "":
+            self._outFileName = "%s.TRF.set" % self.inFileName
+        else:
+            self._outFileName = outFileName
+        
+    def setDoClean(self, doClean):
+        self._doClean = doClean
+        
+    def setVerbosity(self, verbosity):
+        self._verbosity = verbosity
+        
+    def _checkOptions(self):
+        if self.inFileName == "":
+            self._logAndRaise("ERROR: Missing input file name")
+            
+    def _logAndRaise(self, errorMsg):
+        self._log.error(errorMsg)
+        raise Exception(errorMsg)
+    
+    
+    def _launchTRF(self):
+        cmd = "trf %s 2 3 5 80 10 20 %d -h -d" % (self.inFileName, self.maxPeriod)
+        self._log.debug("Running : %s" % cmd)
+        process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        output = process.communicate()
+        self._log.debug("Output:\n%s" % output[0])
+        
+    def _parseTRF(self):
+        self._log.debug("Parsing TRF output")
+        with open( "%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod),'r') as inFile:
+            with open(self._outFileName,'w') as outFile:
+                nbPatterns = 0
+                nbInSeq = 0
+                for line in inFile.readlines():
+                    if line == "":
+                        break
+                    data = line.split(" ")
+                    if len(data) > 1 and "Sequence:" in data[0]:
+                        nbInSeq += 1
+                        seqName = data[1][:-1]
+                    if len(data) < 14:
+                        continue
+                    nbPatterns += 1
+                    consensus = data[13]
+                    copyNb = int( float(data[3]) + 0.5 )
+                    start = data[0]
+                    end = data[1]
+                    outFile.write( "%i\t(%s)%i\t%s\t%s\t%s\n" % ( nbPatterns, consensus, copyNb, seqName, start, end ) )
+        self._log.debug("Finished Parsing TRF output")
+    
+    def _clean(self):
+        try:
+            os.remove("%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod))
+        except:pass
+        
+
+    def run(self):
+        """
+        Launch TRF to detect micro-satellites in sequences.
+        """
+        LoggerFactory.setLevel(self._log, self._verbosity)
+        self._checkOptions()
+        self._log.info("START Launch")
+        self._log.debug("Input file name: %s" % self.inFileName)
+        
+        self._launchTRF()
+        self._parseTRF()
+        
+        if self._doClean:
+            self._log.warning("Files will be cleaned")
+            self._clean()
+        self._log.info("END Launch")
+  
+if __name__ == "__main__":
+    iLaunchTRF = LaunchTRF()
+    iLaunchTRF.setAttributesFromCmdLine()
+    iLaunchTRF.run()        
+