#!/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.seq.FastaUtils import FastaUtils
from commons.core.coord.MatchUtils import MatchUtils
import subprocess
import os
import time
import shutil
from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders

LOG_DEPTH = "repet.base"

##Launch MCL
#
class LaunchMCL(object):
    
    def __init__(self, fastaFileName = "", outFilePrefix = "", inflate = 1.5, covThres = 0.0, isJoined = False, isCluster2Map = False, isClusterConsensusHeaders = False, doClean = False, verbosity = 0):
        self._fastaFileName = fastaFileName
        self.setOutFilePrefix(outFilePrefix)
        self._inflate = inflate
        self._coverageThreshold = covThres
        self._isJoined = isJoined
        self._isCluster2Map = isCluster2Map
        self._isClusterConsensusHeaders = isClusterConsensusHeaders
        self._doClean = doClean
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "Launch MCL clustering program."
        epilog = "\nExample: launch without verbosity and keep temporary files.\n"
        epilog += "\t$ python LaunchMCL.py -i file.fa -v 0\n"
        parser = RepetOptionParser(description = description, epilog = epilog)
        parser.add_option("-i", "--fasta",      dest = "fastaFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
        parser.add_option("-o", "--out",        dest = "outFilePrefix", action = "store",       type = "string", help = "prefix of the output files [default=input fasta file name]",    default = "")
        parser.add_option("-I", "--inflate",    dest = "inflate",       action = "store",       type = "float",  help = "inflate parameter of MCL [optional] [default: 1.5]", default = 1.5)
        parser.add_option("-T", "--coverage",   dest = "coverageThreshold", action = "store",   type = "float",  help = "length coverage threshold (default=0.0, 0.0 <= value <= 1.0)",              default = 0.0)
        parser.add_option("-j", "--join",       dest = "isJoined",          action = "store_true",               help = "join hits after alignement [optional] [default: False]" , default = False)
        parser.add_option("-m", "--map",        dest = "isCluster2Map", action = "store_true",                   help = "generate an additional output file in map format (Warning: only works if MCL's fasta input headers are formated like LTRharvest fasta output)",   default = False)
        parser.add_option("", "--isClusterConsensusHeaders", dest = "isClusterConsensusHeaders", action="store_true", help = "format headers for Cluster Consensus tool", default = False)
        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.setFastaFileName(options.fastaFileName)
        self.setOutFilePrefix(options.outFilePrefix)
        self.setInflate(options.inflate)
        self.setCoverageThreshold(options.coverageThreshold)
        self.setIsJoined(options.isJoined)
        self.setIsCluster2Map(options.isCluster2Map)
        self.setIsClusterConsensusHeaders(options.isClusterConsensusHeaders)
        self.setDoClean(options.doClean)
        self.setVerbosity(options.verbosity)

    def setFastaFileName(self, fastaFileName):
        self._fastaFileName = fastaFileName
        
    def setOutFilePrefix(self, outFilePrefix):
        if outFilePrefix == "":
            self._outFilePrefix = os.path.splitext(self._fastaFileName)[0]
        else:
            self._outFilePrefix = outFilePrefix
            
    def setInflate(self, inflate):
        self._inflate = inflate
        
    def setCoverageThreshold(self, covThres):
        self._coverageThreshold = float(covThres)
    
    def setIsJoined(self, isJoined):
        self._isJoined = isJoined       
        
    def setDoClean(self, doClean):
        self._doClean = doClean
        
    def setIsCluster2Map(self, isCluster2Map):
        self._isCluster2Map = isCluster2Map
        
    def setIsClusterConsensusHeaders(self, isClusterConsensusHeaders):
        self._isClusterConsensusHeaders = isClusterConsensusHeaders
        
    def setVerbosity(self, verbosity):
        self._verbosity = verbosity
        
    def _checkOptions(self):
        if self._fastaFileName == "":
            self._logAndRaise("ERROR: Missing input fasta file name")
        if self._isCluster2Map and self._isClusterConsensusHeaders:
            self._logAndRaise("ERROR: You can't use both '--isClusterConsensusHeaders' and '-m' options")
        if self._coverageThreshold > 1 or self._coverageThreshold < 0:
            self._logAndRaise("ERROR: Coverage Threshold must be in [0.0 , 1.0]")
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
                    
    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        self._checkOptions()
        self._log.info("START Launch MCL")
        self._log.debug("With parameters: -i %s -o %s -I %.2f -T %.2f -j %r -m %r -clusterHeaders %r " % (self._fastaFileName, self._outFilePrefix , self._inflate , self._coverageThreshold, self._isJoined, self._isCluster2Map, self._isClusterConsensusHeaders))
        #self._log.debug("With parameters: -i %s -o %s -I %.2f -T %.2f" % (self._fastaFileName, self._outFilePrefix , self._inflate , self._coverageThreshold))
        self._log.debug("Fasta file name: %s" % self._fastaFileName)
        workingDir = "MCLtmpDirectory"
        if os.path.exists(workingDir):
            self._logAndRaise("ERROR: %s already exists." % workingDir)
        os.mkdir(workingDir)
        os.chdir(workingDir)
        linkToFastaFile = "%s2.fa" % os.path.splitext(self._fastaFileName)[0]
        os.symlink("../%s" % self._fastaFileName, self._fastaFileName)
        fastaFileNameShorten = "%s.shortH" % self._fastaFileName
        iChangeSequenceHeaders = ChangeSequenceHeaders(inFile=self._fastaFileName, format="fasta", step=1, outFile=fastaFileNameShorten, verbosity=self._verbosity - 1)
        iChangeSequenceHeaders.run()
        os.symlink(fastaFileNameShorten, linkToFastaFile)     
        
        self._log.info("START Blaster-Matcher (%s)" % time.strftime("%Y-%m-%d %H:%M:%S"))
        cmd = "LaunchBlaster.py"
        cmd += " -q %s" % fastaFileNameShorten
        cmd += " -s %s" % linkToFastaFile
        cmd += " -a"
        cmd += " 1>&2 >> blasterMatcher.log"
        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)
        outBlasterFileName = "%s.align" % fastaFileNameShorten
        
        cmd = "matcher"
        cmd += " -m %s" % outBlasterFileName
        cmd += " -q %s" % fastaFileNameShorten
        cmd += " -s %s" % linkToFastaFile
        cmd += " -a"
        if self._isJoined:
            cmd += " -j"
        cmd += " 1>&2 >> blasterMatcher.log"
        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 Blaster-Matcher (%s)" % time.strftime("%Y-%m-%d %H:%M:%S"))
        
        outMatcherFileName = "%s.match.tab" % outBlasterFileName
        inputABCFileName = "%s.shortH.abc" % os.path.splitext(fastaFileNameShorten)[0]
        MatchUtils.convertMatchFileIntoABCFileOnQueryCoverage(outMatcherFileName, inputABCFileName, coverage = self._coverageThreshold)
        outMCLPreprocessFileName = "MCLPreprocess.out"
        
        self._log.info("START MCL (%s)" % time.strftime("%Y-%m-%d %H:%M:%S"))
        cmd = "mcxload"
        cmd += " -abc %s" % inputABCFileName
        cmd += " --stream-mirror"
        cmd += " --stream-neg-log10"
        cmd += " -stream-tf 'ceil(200)'"
        cmd += " -o %s" % outMCLPreprocessFileName
        cmd += " -write-tab %s.tab" % outMCLPreprocessFileName
        cmd += " 1>&2 > MCLpreprocess.log"
        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)
        
        outMCLFileName = "out.shortH.mcl"
        cmd = "mcl"
        cmd += " %s" % outMCLPreprocessFileName
        cmd += " -I %s" % self._inflate
        cmd += " -use-tab %s.tab" % outMCLPreprocessFileName
        cmd += " -o %s" % outMCLFileName
        cmd += " 1>&2 > MCL.log"
        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 MCL (%s)" % time.strftime("%Y-%m-%d %H:%M:%S"))

        outFastaFileNameShorten = "%s.fa" % os.path.splitext(outMCLFileName)[0]

        FastaUtils.convertClusterFileToFastaFile(outMCLFileName, fastaFileNameShorten, outFastaFileNameShorten, "MCL", verbosity = self._verbosity - 1)
        
        outFastaFileName = "%s_MCL.fa" % self._outFilePrefix
        linkFileName = "%s.newHlink" % self._fastaFileName
        headerStyle = "A"
        if self._isClusterConsensusHeaders:
            headerStyle = "B"
        iChangeSequenceHeaders = ChangeSequenceHeaders(inFile=outFastaFileNameShorten, format="fasta", step=2, outFile=outFastaFileName, linkFile=linkFileName, whichCluster = headerStyle, verbosity=self._verbosity - 1)
        iChangeSequenceHeaders.run()
        
        if self._isCluster2Map:
            outMapFileName = "%s_MCL.map" % self._outFilePrefix
            FastaUtils.convertClusteredFastaFileToMapFile(outFastaFileName, outMapFileName)
            shutil.move(outMapFileName, "..")

        shutil.move(outFastaFileName, "..")
        os.chdir("..")
        if self._doClean:
            self._log.warning("Working directory will be cleaned")
            shutil.rmtree(workingDir)
        self._log.info("END Launch MCL")

if __name__ == "__main__":
    iLaunch = LaunchMCL()
    iLaunch.setAttributesFromCmdLine()
    iLaunch.run()