def __init__(self, databaseFile):
self._taxonomy = TaxonomyNcbi(databaseFile)
self._ncbidToNcbidParent = dict()
self._closed = False
def __init__(self, databaseFile):
self._taxonomy = TaxonomyNcbi(databaseFile)
self._ncbidToNcbidParent = dict()
self._closed = False
class _TaxonomyWrapper():
"""
Wraps the taxonomy to buffer (speed up) taxonomy calls.
"""
def __init__(self, databaseFile):
self._taxonomy = TaxonomyNcbi(databaseFile)
self._ncbidToNcbidParent = dict()
self._closed = False
def getParent(self, ncbid):
"""
Gets direct parent ncbi taxon id.
"""
if ncbid in self._ncbidToNcbidParent:
return self._ncbidToNcbidParent[ncbid]
else:
parent = self._taxonomy.getParentNcbid(ncbid)
self._ncbidToNcbidParent[ncbid] = parent
return parent
def getDist(self, ncbid, ncbidSet):
"""
Gets the distance between ncbid and the closest clade in the ncbidSet which
represents a path from the root to a clade.
"""
current = ncbid
dist = 0
while (current not in ncbidSet):
if current is None:
sys.stderr.write('Consistency:_TaxonomyWrapper:getDist: current is "None" '
+ str(ncbid) + ' ' + str(ncbidSet) + '\n')
break
current = self.getParent(current)
dist += 1
return dist
def getDistantParent(self, ncbid, intDist):
"""
Gets parent of "ncbid" that is in distance "intDist".
"""
parentNcbid = ncbid
for i in range(int(intDist)):
parentNcbid = self.getParent(parentNcbid)
return parentNcbid
def getDistTowardsRoot(self, ncbid, parentNcbid):
"""
Gets the distance from ncbid to parentNcbid that is its parent and lies on the same path to the root.
"""
current = ncbid
dist = 0
while (current != parentNcbid) and (current != 1):
if current is None:
sys.stderr.write('Consistency:_TaxonomyWrapper:getDistTowardsRoot: current is "None" '
+ str(ncbid) + ' ' + str(parentNcbid) + '\n')
break
current = self.getParent(current)
dist += 1
return float(dist)
def getScientificName(self, ncbid):
return self._taxonomy.getScientificName(ncbid)
def close(self):
""" To free resources. """
self._taxonomy.close()
self._closed = True
def isClosed(self):
return self._closed
class _TaxonomyWrapper():
"""
Wraps the taxonomy to buffer (speed up) taxonomy calls.
"""
def __init__(self, databaseFile):
self._taxonomy = TaxonomyNcbi(databaseFile)
self._ncbidToNcbidParent = dict()
self._closed = False
def getParent(self, ncbid):
"""
Gets direct parent ncbi taxon id.
"""
if ncbid in self._ncbidToNcbidParent:
return self._ncbidToNcbidParent[ncbid]
else:
parent = self._taxonomy.getParentNcbid(ncbid)
self._ncbidToNcbidParent[ncbid] = parent
return parent
def getDist(self, ncbid, ncbidSet):
"""
Gets the distance between ncbid and the closest clade in the ncbidSet which
represents a path from the root to a clade.
"""
current = ncbid
dist = 0
while (current not in ncbidSet):
if current is None:
sys.stderr.write(
'Consistency:_TaxonomyWrapper:getDist: current is "None" '
+ str(ncbid) + ' ' + str(ncbidSet) + '\n')
break
current = self.getParent(current)
dist += 1
return dist
def getDistantParent(self, ncbid, intDist):
"""
Gets parent of "ncbid" that is in distance "intDist".
"""
parentNcbid = ncbid
for i in range(int(intDist)):
parentNcbid = self.getParent(parentNcbid)
return parentNcbid
def getDistTowardsRoot(self, ncbid, parentNcbid):
"""
Gets the distance from ncbid to parentNcbid that is its parent and lies on the same path to the root.
"""
current = ncbid
dist = 0
while (current != parentNcbid) and (current != 1):
if current is None:
sys.stderr.write(
'Consistency:_TaxonomyWrapper:getDistTowardsRoot: current is "None" '
+ str(ncbid) + ' ' + str(parentNcbid) + '\n')
break
current = self.getParent(current)
dist += 1
return float(dist)
def getScientificName(self, ncbid):
return self._taxonomy.getScientificName(ncbid)
def close(self):
""" To free resources. """
self._taxonomy.close()
self._closed = True
def isClosed(self):
return self._closed