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 )
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 = ""
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()
def cmd_start( self, inFileName ): fileName = os.path.basename( inFileName ) pL = programLauncher( fileName ) cmd = pL.launchClustalw( outFileName=inFileName+".fa_aln", run="no" ) return cmd