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