def traverseNewickTreeAndOutputToFile(node):
if len(node.clades) > 0:
traverseNewickTreeAndOutputToFile(node.clades[0])
if len(node.clades) > 1:
traverseNewickTreeAndOutputToFile(node.clades[1])
if node.name != None and len(node.name) > 0:
filteredList = iter(filter(lambda x: x.name == node.name, strains))
foundStrain = next(filteredList, None)
if foundStrain != None:
outputStrainDetailsToFile(outputFileName, foundStrain)
def createAncestor(strain1, strain2, neighborStrain):
globals.ancestralCounter += 1
ancestor = None
ancestralName = 'Ancestor ' + str(globals.ancestralCounter)
ancestralFragments = None
strain1Copy = copy.deepcopy(
strain1) #Do a deep copy of object for when we compare to the neighbor
neighborCopy = copy.deepcopy(
neighborStrain
) #Do a deep copy of the neighbor as well b/c we don't want to store those comparisons in the strain either
print(
'Performing a series of alignments for the following strains: %s, %s' %
(strain1.name, strain2.name))
events, duplicatesStrain1, duplicatesStrain2 = constructEvents(
strain1, strain2)
print('Constructing dot plot for the following strains: %s, %s' %
(strain1.name, strain2.name))
points, lostPoints = normalizeIndexesForDotPlot(events, duplicatesStrain1,
duplicatesStrain2, strain1,
strain2)
createDotPlot(points, strain1, strain2)
createBarGraph(strain1.duplicationCounts,
'Distribution of Duplications for %s' % (strain1.name))
createBarGraph(strain2.duplicationCounts,
'Distribution of Duplications for %s' % (strain2.name))
createBarGraph(
strain1.deletionCounts, 'Distribution of Deletions for %s' %
(strain1.name)) #Remember! Deletions refer to the other strain!
createBarGraph(
strain2.deletionCounts, 'Distribution of Deletions for %s' %
(strain2.name)) #Remember! Deletions refer to the other strain!
#Compute and output the inverted, transposed, and inverted transposed regions
FCR, TR, IR, ITR = determineRegions(points)
#FCR, TR, IR, ITR, LR = computeOperonArrangements(events) OLD VERSION
#inversionDetails1, inversionDetails2 = computeRegionDetails(IR, 'Inversion:')
#transpositionDetails1, transpositionDetails2 = computeRegionDetails(TR, 'Transposition:')
#invertedTransposedDetails1, invertedTransposedDetails2 = computeRegionDetails(ITR, 'Inverted Transposition:')
#Compare one of the siblings to the neighbor if one exists
if neighborCopy != None:
print(
'Now performing a series of alignments between the nighboring strains: %s, %s'
% (strain1Copy.name, neighborCopy.name))
neighborEvents, duplicatesStrain1Copy, duplicatesStrainNeighbor = constructEvents(
strain1Copy, neighborCopy)
print('Constructing dot plot for the neighboring strains: %s, %s' %
(strain1Copy.name, neighborCopy.name))
neighborPoints, neighborLostPoints = normalizeIndexesForDotPlot(
neighborEvents, duplicatesStrain1Copy, duplicatesStrainNeighbor,
strain1Copy, neighborCopy)
#createDotPlot(neighborPoints, strain1Copy, neighborCopy)
#Compute the various regions for the neighbor
#NFCR, NTR, NIR, NITR, NLR = computeOperonArrangements(neighborEvents) OLD VERSION
NFCR, NTR, NIR, NITR = determineRegions(neighborPoints)
ancestralFragments, strain1, strain2 = determineAncestralFragmentArrangementUsingNeighbor(
FCR, TR, IR, ITR, lostPoints, NFCR, NTR, NIR, NITR,
neighborLostPoints, strain1, strain2)
else:
if neighborCopy == None:
print('No neighbor found!')
elif len(TR) == 0 and len(IR) == 0 or len(ITR) == 0:
print('No inverted or transposed regions detected!!')
ancestralFragments, strain2 = determineAncestralFragmentArrangementWithoutNeighbor(
FCR, TR, IR, ITR, lostPoints, strain2)
#Computes the total number of inversions, transpositions, inverted transpositions
globals.inversionCounter += len(IR)
globals.transposedCounter += len(TR)
globals.invertedTransposedCounter += len(ITR)
#Increments the counters for the size distributions for each event type
updateGlobalDeletionCounter(strain1)
updateGlobalDeletionCounter(strain2)
updateGlobalDuplicationCounter(strain1)
updateGlobalDuplicationCounter(strain2)
updateGlobalInversionSizeDistributionCounter(strain1)
updateGlobalInversionSizeDistributionCounter(strain2)
updateGlobalTranspositionSizeDistributionCounter(strain1)
updateGlobalTranspositionSizeDistributionCounter(strain2)
updateGlobalInvertedTranspositionSizeDistributionCounter(strain1)
updateGlobalInvertedTranspositionSizeDistributionCounter(strain2)
#Append all details to file here
outputStrainDetailsToFile(outputFileName, strain1)
outputStrainDetailsToFile(outputFileName, strain2)
ancestor = BacterialStrain(ancestralName, ancestralFragments)
return ancestor