def paths_ratios(self, repertoire):
# Get the dominant genotype network for the repertoire
giant = self.caller.dominant_network(repertoire)
# 'PathAnalyzer' object
path_analyzer = PathAnalyzer(giant, self.netBuilder,
self.deltaDict[repertoire])
# Run shortest paths calculation for all paths; regardless of path length.
# This sets the 'max_path_length' value.
path_analyzer.getAccessiblePaths()
# Length of the longest path in the network
max_path_length = path_analyzer.max_path_length
# Compute the ratio of accessible paths for all path lengths in range:
# [2, max_path_length].
# Set dict {path_length : ratio}
giant["Ratio_of_accessible_mutational_paths"] = {
i: path_analyzer.getAccessiblePaths(i)
for i in xrange(2, max_path_length + 1)
}
def __init__(self, network, netUtils, seqToEscrDict, delta, bitManip) :
# Store reference to the network object
self.network = network
# Store reference to the netUtils object
self.netUtils = netUtils
# Create the peak analyzer
self.peakAnalyzer = PeakAnalyzer(network, netUtils, delta)
# Create the path analyzer
self.pathAnalyzer = PathAnalyzer(network, netUtils, delta)
# Create the epistasis analyzer
self.epiAnalyzer = EpistasisAnalyzer(network, netUtils,
seqToEscrDict, delta, bitManip)
# Get a reference to the BitSeqManipulator in use
self.bitManip = self.netUtils.bitManip
class Landscape :
# Constructor
def __init__(self, network, netUtils, seqToEscrDict, delta, bitManip) :
# Store reference to the network object
self.network = network
# Store reference to the netUtils object
self.netUtils = netUtils
# Create the peak analyzer
self.peakAnalyzer = PeakAnalyzer(network, netUtils, delta)
# Create the path analyzer
self.pathAnalyzer = PathAnalyzer(network, netUtils, delta)
# Create the epistasis analyzer
self.epiAnalyzer = EpistasisAnalyzer(network, netUtils,
seqToEscrDict, delta, bitManip)
# Get a reference to the BitSeqManipulator in use
self.bitManip = self.netUtils.bitManip
# ----------------------------------------------------------------
# Peak analysis methods
# ----------------------------------------------------------------
def getPeaks(self, recompute) :
return self.peakAnalyzer.getPeaks(recompute)
# ----------------------------------------------------------------
# Path analysis methods
# ----------------------------------------------------------------
def getAccessiblePaths(self, pathLength=0):
return self.pathAnalyzer.getAccessiblePaths(pathLength)
# ----------------------------------------------------------------
# Epistasis analysis methods
# ----------------------------------------------------------------
def getEpistasis(self) :
return self.epiAnalyzer.getEpiAll()
# ----------------------------------------------------------------
# Calculate mutational distances from summit for all vertices
# ----------------------------------------------------------------
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 ]