#!/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")