annotate commons/launcher/LaunchMummerPlot.py @ 18:94ab73e8a190

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#! /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. 
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# 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
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from commons.core.checker.CheckerUtils import CheckerUtils
from commons.core.utils.FileUtils import FileUtils
from commons.core.utils.RepetOptionParser import RepetOptionParser
import subprocess
from commons.core.LoggerFactory import LoggerFactory
import os
import shutil
  
LOG_DEPTH = "repet.tools"  
  
class LaunchMummerPlot(object):

    def __init__(self, inputFileName="", queryFileName="", refFileName ="", prefix = None, fat=False, filter=False,clean=False, verbosity=0):
        self._inputFileName = inputFileName
        self._queryFileName = queryFileName
        self._refFileName = refFileName
        self._prefix = prefix
        self._fat = fat
        self._filter = filter
        self.doClean = clean
        self.verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
             
    def setAttributesFromCmdLine(self):
        description = "LaunchMummerPlot runs the MummerPlot program (part of the mummer package) ."    
        parser = RepetOptionParser(description = description)
        parser.add_option("-i", "--input", dest="inputFileName", default = None,  action="store", type="string", help="input file[mandatory] [format: delta]")      
        parser.add_option("-q", "--Qfile", dest="queryFileName", default = None,  action="store", type="string", help="Plot an ordered set of reference sequences from Qfile [optional] [format: fasta]")
        parser.add_option("-r", "--Rfile", dest="refFileName", default = None,  action="store", type="string", help="Plot an ordered set of reference sequences from Rfile [optional] [format: fasta]")
        parser.add_option("-p", "--prefix", dest="prefix", default = None,  action="store", type="string", help="prefix name [mandatory]")
        parser.add_option("-o","--fat", dest="fat",action="store_true", help="Layout sequences using fattest alignment only[optional] ")
        parser.add_option("-s","--filter", dest="filter",action="store_true", help="Only display .delta alignments which represent the 'best' hit [optional] ")      
        parser.add_option("-c", "--clean", dest = "clean", help = "clean temporary files", default = False, action="store_true")  
        parser.add_option("-v", "--verbosity", dest="verbosity", default = 0,  action="store", type="int", help="verbosity [optional] ")
        
        (self._options, args) = parser.parse_args()
        self._setAttributesFromOptions(self._options)

    def _setAttributesFromOptions(self, options):
        self._inputFileName = options.inputFileName
        self._queryFileName = options.queryFileName
        self._refFileName = options.refFileName
        self._prefix = options.prefix
        self._fat = options.fat
        self._filter = options.filter
        self.verbosity = options.verbosity
        
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
            
    def checkOptions(self):  
        if self._inputFileName != "":
            if not FileUtils.isRessourceExists(self._inputFileName):
                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._inputFileName)
        else:
            self._logAndRaise("ERROR: No specified --query option!")     
        
        if self._queryFileName != "":
            if not FileUtils.isRessourceExists(self._queryFileName):
                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName)
        
        if self._refFileName != "":
            if not FileUtils.isRessourceExists(self._refFileName):
                self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName)
                
    def clean(self):
        try:
            os.remove("%s.filter" % self._prefix)
        except Exception as inst: 
            self._log.error(inst)
        try:
            os.remove("%s.fplot" % self._prefix)
        except Exception as inst: 
            self._log.error(inst)
        try:
            os.remove("%s.rplot" % self._prefix)
        except Exception as inst: 
            self._log.error(inst)
                                
    def run(self):
        if not CheckerUtils.isExecutableInUserPath("mummerplot") :
            self._logAndRaise("ERROR: mummerplot must be in your path")
        self.checkOptions()
        
        ref=""
        if self._refFileName != "":
            ref = "-R %s"  % self._refFileName
           
        query=""
        if self._queryFileName != "":
            query = "-Q %s"  % self._queryFileName
           
        fat = ""
        if self._fat:
            fat =  "--fat"
            
        filter = ""
        if self._filter:
            filter = "-f" 
            
        prefix = ""
        if self._prefix is not None:
            prefix = "--prefix=%s" %(self._prefix)
            
        cmd = "mummerplot %s %s %s %s %s %s --png" % (self._inputFileName, prefix, ref, query, fat, filter)
        self._log.debug("Running mummerplot with following commands : %s" %cmd)
        cmd = cmd.split()         
        process = subprocess.Popen(cmd)
        process.wait()
        
        self.clean()
        return process.returncode
            
if __name__ == "__main__":
    iLaunchNucmer = LaunchMummerPlot()
    iLaunchNucmer.setAttributesFromCmdLine()
    iLaunchNucmer.run()