#!/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 os
from commons.core.seq.Bioseq import Bioseq

LOG_DEPTH = "repet.core.launchers"

from commons.core.seq.BioseqDB import BioseqDB
from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders


class LaunchRefAlign(object):
    """
    Launch 'refalign' to build a master-slave multiple sequence alignment.
    """
    def __init__(self, inputFileName="", outFileName="", gapSize=10, match=10, mismatch=8, gapOpen=16, gapExtend=4, refseqName="", keepRefseq =False, verbosity=3 ):
        self.inputFileName = inputFileName
        self.outFileName=outFileName
        self.gapSize = gapSize
        self.match = match
        self.mismatch = mismatch
        self.gapOpen = gapOpen
        self.gapExtend = gapExtend
        self.gapExtend = gapExtend
        self.refseqName = refseqName
        self.keepRefseq = keepRefseq
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "usage: LaunchRefalign.py [ options ]"
        epilog = "\n -h: this help\n"
        epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
        epilog += "\t -r: keep the reference sequence"
        epilog += "\t -o: name of the output file (default=inFileName+'.fa_aln')"
        epilog += "\t -v: verbosity (default=0)"
        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("-r", "--keepRefseq", dest = "keepRefseq",    action = "store_true",                   help = "keep reference sequence [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.inputFileName = options.inputFileName
        self.setOutFileName = options.outFileName
        self.keepRefseq = options.keepRefseq
        self._verbosity = options.verbosity

    def _checkOptions(self):
        if self.inputFileName == "":
            self._logAndRaise("ERROR: Missing input file name")
    
        if self.outFileName == "":
            self.outFileName = "%s.fa_aln" % (self.inputFileName)
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
         
    def _prepareRefAlign(self):
        self.shortInputFileName = self.inputFileName+".shortH" 
        self.refFileName= self.shortInputFileName + ".ref"
        self.cpyFileName=self.shortInputFileName + ".cpy"
        
        file_db = open(self.shortInputFileName)
        file_ref = open(self.refFileName,"w")
        file_cpy = open(self.cpyFileName,"w")
        
        self._numseq=0
        while 1:
            seq=Bioseq()
            seq.read(file_db)
            if seq.sequence==None:
                break
            self._numseq+=1
            if self._numseq==1:
                seq.write(file_ref)
            else:
                seq.write(file_cpy)
        file_db.close()
        file_ref.close()
        file_cpy.close()
    
    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()
        
        bsDB = BioseqDB(self.inputFileName+".shortH")
        bsDB.upCase()
        bsDB.save(self.inputFileName+".shortHtmp")
        del bsDB
        os.rename(self.inputFileName+".shortHtmp", self.inputFileName+".shortH")
        
    def _renameHeaders(self):
        self.csh.setInputFile(self.inputFileName+".shortH.fa_aln")
        self.csh.setFormat("fasta")
        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 LaunchRefAlign")
        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()
        if self.keepRefseq:
            self.refseqName="seq1"
        self._prepareRefAlign()
        
        if self._numseq > 1:
            cmd = "refalign %s %s -m %d -l %d -d %d -g %d -e %d" % (self.refFileName, self.cpyFileName, self.match, self.gapSize, self.mismatch, self.gapOpen, self.gapExtend)
            
            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)
            refseqNameParam = ""
            if self.refseqName != "":
                refseqNameParam = "-r %s " % (self.refseqName)
            outFileName = self.inputFileName+".shortH.fa_aln"
            #self.cpyFileName = os.path.join(os.getcwd(),os.path.basename(self.cpyFileName))
            
            self._log.info("Copy file path %s " % self.cpyFileName)
            print("Copy file path %s " % self.cpyFileName)
            cmd = "refalign2fasta.py -i %s.aligner %s-g d -o %s -v 1" % (self.cpyFileName, refseqNameParam, outFileName)
            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])
            
            if process.returncode != 0:
                self._logAndRaise("ERROR when launching '%s'" % cmd)
                
            cmd = "rm -f "+ self.refFileName + " " + self.cpyFileName + " " + self.cpyFileName + ".aligner " + self.cpyFileName + ".oriented " + self.cpyFileName + ".refalign.stat"
            os.system(cmd)
            
        else:
            self._logAndRaise("Only one sequence available")
            cmd = "echo empty"
            
        self._renameHeaders()
        
        for fileName in [self.inputFileName + ".shortH", self.inputFileName + ".shortHlink", self.inputFileName + ".shortH.fa_aln"]:
            os.remove(fileName)
        self._log.info("END LaunchRefAlign")
        return 0
        

if __name__ == "__main__":
    iLaunchRefAlign = LaunchRefAlign()
    iLaunchRefAlign.setAttributesFromCmdLine()
    iLaunchRefAlign.run()