Ejemplo n.º 1
0
 def prepareProfilesBank(self, launch_1, launch_2, config, cDir, verbose = 0):
     bank = self._getBankBaseName(config)
     prg = "hmmpress"
     pL = programLauncher()
     if verbose > 0:
         print "prepare bank '%s'..." % ( bank ); sys.stdout.flush()
     cmd = ""
     cmd += prg + " -f "
     cmd += "%s/%s" % ( cDir, bank )
     
     pL.launch( prg, cmd )
Ejemplo n.º 2
0
 def __init__( self ):
     """
     Constructor.
     """
     self._inFileName = ""
     self._identityThreshold = 95
     self._coverageThreshold = 0.9
     self._bothSeq = "T"
     self._filterUnclusteredSeq = False
     self._outFilePrefix = ""
     self._clean = False
     self._verbose = 0
     self._pL = programLauncher()
     self._tmpFileName = ""
Ejemplo n.º 3
0
        logging.info( "finished" )
        sys.exit(0)

    nbSeqSbj = FastaUtils.dbSize( sbjFileName )
    if sbjFileName != qryFileName:
        nbSeqSbj = FastaUtils.dbSize( sbjFileName )
        if nbSeqSbj == 0:
            string = "subject file is empty"
            logging.info( string )
            print "WARNING: %s" % ( string )
            logging.info( "finished" )
            sys.exit(0)

    #--------------------------------------------------------------------------

    pL = programLauncher()
    uniqTmpDir = "tmp%s" % ( uniqId )
    if os.path.exists( uniqTmpDir ):
        shutil.rmtree( uniqTmpDir )
    os.mkdir( uniqTmpDir )
    os.chdir( uniqTmpDir )
    os.system( "ln -s ../%s ." % ( qryFileName ) )
    if sbjFileName != qryFileName:
        os.system( "ln -s ../%s ." % ( sbjFileName ) )
    os.system( "ln -s ../%s ." % ( logFileName ) )
    if useCluster:
        os.system( "ln -s ../%s ." % ( configFileName ) )
        config = ConfigParser.ConfigParser()
        config.readfp( open(configFileName) )
        queue = config.get("classif_consensus", "resources")
        cDir = os.getcwd()
Ejemplo n.º 4
0
 def cmd_start( self, inFileName ):
     fileName = os.path.basename( inFileName )
     pL = programLauncher( fileName )
     cmd = pL.launchClustalw( outFileName=inFileName+".fa_aln", run="no" )
     return cmd