#!/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()