view commons/launcher/LaunchPromer.py @ 31:0ab839023fe4

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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". 
#
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# 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
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# with loading,  using,  modifying and/or developing or reproducing the
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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
  
LOG_DEPTH = "repet.tools"  
  
class LaunchPromer(object):

    def __init__(self,queryFileName="", refFileName ="", prefix = None, genCoords=False, showCoords = False, mum=False, maxGaps=30, minMatch=6, nooptimize=False,mincluster=20, verbosity=0):
        self._queryFileName = queryFileName
        self._refFileName = refFileName
        self._prefix = prefix
        self._genCoords = genCoords
        self._showCoords = showCoords
        self._mum = mum
        self._maxgaps = maxGaps
        self._minMatch = minMatch
        self._nooptimize = nooptimize
        self._mincluster = mincluster
        self.verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
        
    def setMincluster(self, value):
        self._mincluster = value
    def getMincluster(self):
        return self._mincluster
    
    mincluster = property(getMincluster, setMincluster)
         
    def setAttributesFromCmdLine(self):
        description = "LaunchPromer runs the Promer program (part of the mummer package) ."    
        parser = RepetOptionParser(description = description)
        parser.add_option("-q", "--query", dest="queryFileName", default = "",  action="store", type="string", help="input query file [compulsory] [format: fasta]")
        parser.add_option("-r", "--ref", dest="refFileName", default = "",  action="store", type="string", help="input ref file [compulsory] [format: fasta]")
        parser.add_option("-p", "--prefix", dest="prefix", default = None,  action="store", type="string", help="prefix name [optional]")
        parser.add_option("-o","--gencoords", dest="genCoords",action="store_true", help="generate coords file with minimal option (show-coords -r) [optional] ")
        parser.add_option("-s","--showcoords", dest="showCoords",action="store_true", help="generate coords file with: show-coords -r -c -l -d -I 50 -L 100 -T [optional] ")        
        parser.add_option("-m", "--mum", dest="mum",  action="store_true", help="Use anchor matches that are unique in both the reference and query [optional] ")      
        parser.add_option("-g", "--maxgaps", dest="maxgaps", default = 30,  action="store", type="int", help="Maximum gap between two adjacent matches in a cluster (default 30) [optional] ")
        parser.add_option("-l", "--minmatch", dest="minMatch", default = 6,  action="store", type="int", help="Minimum length of an maximal exact match (default 6) [optional] ")
        parser.add_option("-n", "--nooptimize", dest="nooptimize", action="store_true", help="nooptimize (default --optimize) [optional] ")  
        parser.add_option("-j", "--mincluster", dest="mincluster", default = 20,  action="store", type="int", help="Minimum length of a cluster of matches (default 20) [optional] ")
        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._queryFileName = options.queryFileName
        self._refFileName = options.refFileName
        self._prefix = options.prefix
        self._genCoords = options.genCoords
        self._showCoords = options.showCoords
        self._mum = options.mum  
        self._maxgaps = options.maxgaps
        self._minMatch = options.minMatch
        self._nooptimize =  options.nooptimize
        self._mincluster = options.mincluster
        self.verbosity = options.verbosity
        
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
            
    def checkOptions(self):       
        if self._queryFileName != "":
            if not FileUtils.isRessourceExists(self._queryFileName):
                self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName)
        else:
            self._logAndRaise("ERROR: No specified --query option!")
        
        if self._refFileName != "":
            if not FileUtils.isRessourceExists(self._refFileName):
                self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName)
        else:
            self._logAndRaise("ERROR: No specified --ref option!")
                                
    def run(self):
        if not CheckerUtils.isExecutableInUserPath("promer") :
            self._logAndRaise("ERROR: promer must be in your path")
        self.checkOptions()
        
        genCoords = ""
        if self._genCoords:
            genCoords = "-o"     
        mum = ""
        if self._mum:
            mum =  "--mum"
        nooptimize = "--optimize"
        if self._nooptimize:
            nooptimize = "--nooptimize" 
        prefix = ""
        if self._prefix is not None:
            prefix = "--prefix=%s" %(self._prefix)
            
        cmd = "promer %s %s %s %s %s -g=%d -l=%d %s -c=%d" % (self._refFileName,self._queryFileName, prefix, genCoords, mum, self._maxgaps, self._minMatch, nooptimize, self._mincluster)
        self._log.debug("Running promer with following commands : %s" %cmd)
        cmd = cmd.split()         
        process = subprocess.Popen(cmd)
        process.wait()
        
        if self._showCoords:
            #use of os.system because redirect on process is broken in python < 3.0
            cmd = "show-coords -r -c -l -d -I 50 -L 100 -T %s.delta > %s.coords" % (self._prefix, self._prefix)
            os.system(cmd)

        return process.returncode
            
if __name__ == "__main__":
    iLaunchPromer = LaunchPromer()
    iLaunchPromer.setAttributesFromCmdLine()
    iLaunchPromer.run()