def getAccessiblePaths(self, pathLength=0):
# Stats for the entire network
totalPaths = 0 # Total mutational paths (only shortest)
allAccPaths = 0 # No. of accessible paths (only shortest)
# Get the sequence with the highest score. This sequence
# will represent the global peak. All paths use this
# sequence as the target.
summit = Utils.getSeqWithMaxScore(self.network, self.bitManip.seqLength)
# Get the vertex object that represents the summit
trgtVrtx = self.netUtils.getVertex(summit, self.network)
# Store a copy of the summit
self.summitId = trgtVrtx.index
# Get a list of all sequences in the network
sequences = self.network.vs["sequences"]
# Remove the target itself
sequences.remove(summit)
# For each sequence in the network
for source in sequences:
# If we only need to calculate all accessible paths, regardless
# of the path length,
if pathLength == 0:
# Get all shortest paths as well as all accessible
# shortest paths from source to summit
self.getShortestAccPaths(source, trgtVrtx, pathLength)
else: # Ratios should be calculated
shrtPaths, accPaths = self.getShortestAccPaths(source,
trgtVrtx,
pathLength + 1)
# If at least one shortest path of length == 'pathLength' was
# found,
if shrtPaths:
# Increment the counts
totalPaths += float(len(shrtPaths))
allAccPaths += float(len(accPaths))
try:
return float(allAccPaths) / float(totalPaths)
except ZeroDivisionError:
return 0
def populateDistsToSummit(self) :
# Convenient handle for bitManip
bm = self.bitManip
# Get the summit sequence
summit = Utils.getSeqWithMaxScore(self.network,
self.bitManip.seqLength)
# Get vertex that represents summit
trgtVrtx = self.netUtils.getVertex(summit, self.network)
# Reference to the list of sequences in the network
vertices = [ self.netUtils.getVertex(seq, self.network) \
for seq in self.network.vs["sequences"] ]
self.network.vs["Distance from Summit"] = \
[ len(self.network.get_shortest_paths(srcVrtx, to=trgtVrtx, \
weights=None, mode=igraph.OUT, output="epath")[0]) \
for srcVrtx in vertices ]
def getAnalysisTypes():
return Utils.reverseDict(AnalysisConstants.analysisToDesc)
