def __init__(self,
organisms,
ncpus=1,
evalue=1e-10,
recover=False,
prefix='',
matrix='BLOSUM80',
queue=Queue.Queue()):
CommonMultiProcess.__init__(self, ncpus, queue)
# Blast
self.organisms = list(organisms)
self.dbs = {}
self._prot2orgs = {}
self.out = []
self.evalue = float(evalue)
# TODO: implement recovery
self.recover = recover
#
self.results = {}
self._blast = Blaster()
self._pangenomeroom = None
self.prefix = prefix.rstrip('_')
self.matrix = matrix
self._already = set()
# Results
self.orthologs = {}
self.core = []
self.accessory = []
self.unique = []
def __init__(self,
query,
target,
ncpus=1,
evalue=1e-50,
buildDB=True,
bbh=True,
recover=False,
queue=Queue.Queue()):
CommonMultiProcess.__init__(self, ncpus, queue)
# Blast
self.query = query
if buildDB:
self.target = target
self.db = None
else:
self.target = None
self.db = target
self.out = []
self.evalue = float(evalue)
self.bbh = bool(bbh)
self.recover = recover
self.ncpus = int(ncpus)
self._kohits = []
self.results = {}
self._keggroom = None
self._blast = Blaster()
def __init__(self,organisms,
ncpus=1,evalue=1e-10,
recover=False,prefix='',
matrix='BLOSUM80',queue=Queue.Queue()):
CommonMultiProcess.__init__(self,ncpus,queue)
# Blast
self.organisms = list(organisms)
self.dbs = {}
self._prot2orgs = {}
self.out = []
self.evalue = float(evalue)
# TODO: implement recovery
self.recover = recover
#
self.results = {}
self._blast = Blaster()
self._pangenomeroom = None
self.prefix = prefix.rstrip('_')
self.matrix = matrix
self._already = set()
# Results
self.orthologs = {}
self.core = []
self.accessory = []
self.unique = []
def __init__(self,project, paths,
ncpus=1,queue=Queue.Queue()):
CommonMultiProcess.__init__(self,ncpus,queue)
# DB name
self._project = project
# To-be-analyzed pathways
self.paths = paths
# path_id --> dpangenome
self.result = {}
def __init__(self,query,target,
ncpus=1,evalue=1e-50,
buildDB=True,bbh=True,recover=False,queue=Queue.Queue()):
CommonMultiProcess.__init__(self,ncpus,queue)
# Blast
self.query = query
if buildDB:
self.target = target
self.db = None
else:
self.target = None
self.db = target
self.out = []
self.evalue = float(evalue)
self.bbh = bool(bbh)
self.recover = recover
self.ncpus = int(ncpus)
self._kohits = []
self.results = {}
self._keggroom = None
self._blast = Blaster()