--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/LaunchPhyML.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,177 @@
+#!/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.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
+import subprocess
+import os
+from commons.core.seq.Bioseq import Bioseq
+import shutil
+
+LOG_DEPTH = "repet.core.launchers"
+
+
+
+class LaunchPhyML(object):
+    """
+    Launch 'PhyML'
+    """
+    def __init__(self, inputFileName="", outFileName="",dataType= "nt", interleavedFormat= True, nbDataSets=1, nbBootDataSets=0, substModel="HKY85", ratioTsTv=4.0, propInvSites= 0.0, nbCat=1, gammaParam=1.0, startTree="BIONJ", paramOptimisation = "tlr", clean=False, verbosity=3 ):
+        self.inputFileName = inputFileName
+        self.outFileName=outFileName
+        self.dataType = dataType                    #"nt or aa"
+        self._setSeqFormat(interleavedFormat)       #if False -q"
+        self.nbDataSets = nbDataSets
+        self.nbBootDataSets = nbBootDataSets
+        self.substModel = substModel
+        self.ratioTsTv = ratioTsTv
+        self.propInvSites = propInvSites            # propInvSites="e" replaced by 0.0; should be in [0-1]
+        self.nbCat = nbCat                          # Number of categories less than four or higher than eight are not recommended.
+        self.gammaParam = gammaParam
+        self.startTree = startTree                  #by default is BIONJ used reformatedInputFileName+"_phyml_tree.txt" instead
+        self.paramOptimisation = paramOptimisation  # used instead of self.optTopology="y", self.optBranchRate="y" 
+                                                    #This option focuses on specific parameter optimisation.
+                                                    #tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
+                                                    #tl  : tree topology and branch length are optimised.
+                                                    #lr  : branch length and rate parameters are optimised.
+                                                    #l   : branch length are optimised.
+                                                    #r   : rate parameters are optimised.
+                                                    #n   : no parameter is optimised.
+
+        self._clean = clean
+        self._verbosity = verbosity
+        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
+    
+    def _setSeqFormat(self, interleavedFormat):
+        if not (interleavedFormat) :
+            self.seqFormat = " -q"
+        else :
+            self.seqFormat = ""
+            
+    def setAttributesFromCmdLine(self):
+        description = "usage: LaunchPhyML.py [ options ]"
+        epilog = "\n -h: this help\n"
+        epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
+        epilog += "\n\t"
+        parser = RepetOptionParser(description = description, epilog = epilog)
+        parser.add_option("-i", "--fasta",      dest = "inputFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
+        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.out]", default = "")
+        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.inputFileName = options.inputFileName
+        self.setOutFileName = options.outFileName
+        self._verbosity = options.verbosity
+
+    def _checkOptions(self):
+        if self.inputFileName == "":
+            self._logAndRaise("ERROR: Missing input file name")
+    
+        if self.outFileName == "":
+            self.outFileName = "%s_phyml.newick" % (self.inputFileName)
+            
+    def _logAndRaise(self, errorMsg):
+        self._log.error(errorMsg)
+        raise Exception(errorMsg)
+         
+    def _shortenHeaders(self):
+        self.csh = ChangeSequenceHeaders()
+        self.csh.setInputFile(self.inputFileName)
+        self.csh.setFormat("fasta")
+        self.csh.setStep(1)
+        self.csh.setPrefix("seq")
+        self.csh.setLinkFile(self.inputFileName+".shortHlink")
+        self.csh.setOutputFile(self.inputFileName+".shortH")
+        self.csh.setVerbosityLevel(self._verbosity-1)
+        self.csh.run()
+        self.shortInputFileName = self.inputFileName+".shortH" 
+        
+    def _renameHeaders(self):
+        self.csh.setInputFile(self.phyml_tree)
+        self.csh.setFormat("newick")
+        self.csh.setStep(2)
+        self.csh.setLinkFile(self.inputFileName+".shortHlink" )
+        self.csh.setOutputFile(self.outFileName)
+        self.csh.setVerbosityLevel(self._verbosity-1)
+        self.csh.run()
+          
+    def run(self):
+        LoggerFactory.setLevel(self._log, self._verbosity)
+        self._checkOptions()
+        self._log.info("START LaunchPhyML")
+        self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName))
+        
+        inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName))
+        if not os.path.exists(inputFileName):
+            os.symlink(self.inputFileName, inputFileName)
+        self.inputFileName = inputFileName
+        
+        self._shortenHeaders()
+
+        cmd = "sreformat phylip %s" % (self.shortInputFileName)
+        
+        with open (self.reformatedInputFileName, "w") as fPhylip :
+            
+            process = subprocess.Popen(cmd.split(' '), stdout= fPhylip , stderr=subprocess.PIPE)
+            self._log.debug("Running : %s" % cmd)
+            output = process.communicate()
+            self._log.debug("Output:\n%s" % output[0])
+            if process.returncode != 0:
+                self._logAndRaise("ERROR when launching '%s'" % cmd)
+        
+        self.reformatedInputFileName = "%s.phylip" % self.shortInputFileName
+        self.phyml_tree = "%s_phyml_tree.txt" %self.reformatedInputFileName 
+        cpyPhyml_tree = "%s_cpy" %self.phyml_tree
+        shutil.copyfile(self.phyml_tree,cpyPhyml_tree)
+                          
+        cmd = "phyml -i %s -d %s%s -n %d -b %d -m %s -t %f -v %f -c %d -a %f -u %s -o %s" % (self.reformatedInputFileName, self.dataType, self.seqFormat, self.nbDataSets,self.nbBootDataSets,self.substModel, self.ratioTsTv, self.propInvSites,self.nbCat,self.gammaParam, cpyPhyml_tree , self.paramOptimisation )
+        print cmd    
+        process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        self._log.debug("Running : %s" % cmd)
+        output = process.communicate()
+        self._log.debug("Output:\n%s" % output[0])
+        if process.returncode != 0:
+            self._logAndRaise("ERROR when launching '%s'" % cmd)
+        
+        self._renameHeaders()
+        
+        if self._clean:
+            for f in [ self.shortInputFileName, self.inputFileName+".shortHlink", self.inputFileName+".shortH.phylip",self.inputFileName+".shortH.phylip_phyml_lk.txt", self.phyml_tree ]:
+                os.remove(f)
+            os.system( "mv %s.phylip_phyml_stat.txt %s_phyml.txt" % ( self.shortInputFileName, self.inputFileName ) )
+        
+        self._log.info("Finished running LaunchPhyML")
+        
+