def makecompletegraph(self):
"""
"""
OrganismGraph.makecompletegraph(self)
for u,v in self.weights.keys():
if not self._edge_binary_entropies.has_key((u,v)):
self._edge_binary_entropies[(u,v)] = (1.0,1.0)
def __init__(self,tcode_5p_windowsize=201,tcode_3p_windowsize=201):
"""
Initialize a AlignedStartCodonGraph
"""
OrganismGraph.__init__(self)
self._tcode5pscore = {}
self._tcode3pscore = {}
self._TCODE_5P_WINDOWSIZE = tcode_5p_windowsize
self._TCODE_3P_WINDOWSIZE = tcode_3p_windowsize
def __init__(self,max_node_count=None,min_pssm_score=None,aligned_site_aa_offset=None):
"""
Initialize a AlignedPssmObjectGraph
"""
OrganismGraph.__init__(self)
self._node_pssm = {}
self._node_object = {}
self.MIN_PSSM_SCORE = min_pssm_score
self.MAX_NODE_COUNT = max_node_count
self.ALIGNED_SITE_AA_OFFSET = aligned_site_aa_offset
def __init__(self):
"""
Initialize a GeneTreeGraph
"""
# Initialize as an OrganismGraph
OrganismGraph.__init__(self)
# self.weights contains identityscores
# add similar dicts for aa_identity, bitscore_ratios and nt_identity
self._aa_identity_percentages = {}
self._bitscore_ratios = {}
self._nt_identity_percentages = {}
def __init__(self):
"""
Initialize a GeneTreeGraph
"""
# Initialize as an OrganismGraph
OrganismGraph.__init__(self)
# self.weights contains identityscores
# add similar dicts for aa_identity, bitscore_ratios and nt_identity
self._aa_identity_percentages = {}
self._bitscore_ratios = {}
self._nt_identity_percentages = {}
def __init__(self):
"""
Initialize a PacbpCollectionGraph
"""
# Initialize as an OrganismGraph
OrganismGraph.__init__(self)
# set extra attributes
self._node_object = {}
self._node_pssm = {}
# needed for backwards compatibilty with PacbpCollectionGraph, CodingBlockGraph
self.pacbps = {}
self._omsr = {}
def pairwisecrosscombinations_organism(self,order_by=None):
"""
Get unique cross combinations of organisms in the graph, ordered on request
@rtype: list
@return: list of all unique combinations of two organisms
@attention: returns ORDERED list of ORDERED tuples of organism combinations
@attention: orderability overwrites OrganismGraph.pairwisecrosscombinations_organism
@attention: use order_by='identity' to obtain identity ordering except alphabetical
"""
if order_by == 'identity':
combinations = []
for a in self.organism_set():
for b in self.organism_set():
if a == b: continue
combi = [a,b]
combi.sort()
if combi == [a,b]:
wt = self.weights[(a,b)]
combinations.append( ( wt, tuple(combi) ) )
# return the ordered (by wt) list of unique combinations
combinations.sort()
combinations.reverse()
return [ combi for (wt,combi) in combinations ]
else:
# return basal (alphabetical) ordered pairs of organisms
return OrganismGraph.pairwisecrosscombinations_organism(self)
def pairwisecrosscombinations_organism(self, order_by=None):
"""
Get unique cross combinations of organisms in the graph, ordered on request
@rtype: list
@return: list of all unique combinations of two organisms
@attention: returns ORDERED list of ORDERED tuples of organism combinations
@attention: orderability overwrites OrganismGraph.pairwisecrosscombinations_organism
@attention: use order_by='identity' to obtain identity ordering except alphabetical
"""
if order_by == 'identity':
combinations = []
for a in self.organism_set():
for b in self.organism_set():
if a == b: continue
combi = [a, b]
combi.sort()
if combi == [a, b]:
wt = self.weights[(a, b)]
combinations.append((wt, tuple(combi)))
# return the ordered (by wt) list of unique combinations
combinations.sort()
combinations.reverse()
return [combi for (wt, combi) in combinations]
else:
# return basal (alphabetical) ordered pairs of organisms
return OrganismGraph.pairwisecrosscombinations_organism(self)
def __init__(self):
"""
Initialize a PssmObjectCollectionGraph; objects on orfs on pacbporfs (splice sites, start sites, stop sites)
"""
OrganismGraph.__init__(self)
self._node_pssm = {}
self._node_object = {}
self.MIN_PSSM_SCORE = None
# list to store aligned sites graphs
self.alignedsites = []
# dictionary keeping track of considered range
self._organism_consideredrange = {}
# Attributes storing information for thresholds of
# how this collection was generated
self.ALIGNED_SITE_AA_OFFSET = None
self.MIN_PSSM_SCORE = None
def __init__(self,cbg,tcode_5p_windowsize=201,tcode_3p_windowsize=201):
"""
Initialize a AlignedStopCodonGraph
"""
OrganismGraph.__init__(self)
# attribute for storing the CBG itself
self._codingblockgraph = cbg
# attributes for TCODE data
self._tcode5pscore = {}
self._tcode3pscore = {}
self._TCODE_5P_WINDOWSIZE = tcode_5p_windowsize
self._TCODE_3P_WINDOWSIZE = tcode_3p_windowsize
# is_optimal_xxx thresholds
self._optimal_min_tcode = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_TCODE
self._optimal_max_tcode = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_TCODE
self._optimal_min_weight = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_WEIGHT
self._optimal_max_weight = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_WEIGHT
self._optimal_min_gtgweakest = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_GTGWEAKEST
self._optimal_max_gtgweakest = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_GTGWEAKEST
# run function codingblock_collectionharvesting.align_stop_codons
# to fully initialize the object
self = codingblock_collectionharvesting.align_stop_codons(cbg,self)
def __init__(self, cbg, tcode_5p_windowsize=201, tcode_3p_windowsize=201):
"""
Initialize a AlignedStopCodonGraph
"""
OrganismGraph.__init__(self)
# attribute for storing the CBG itself
self._codingblockgraph = cbg
# attributes for TCODE data
self._tcode5pscore = {}
self._tcode3pscore = {}
self._TCODE_5P_WINDOWSIZE = tcode_5p_windowsize
self._TCODE_3P_WINDOWSIZE = tcode_3p_windowsize
# is_optimal_xxx thresholds
self._optimal_min_tcode = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_TCODE
self._optimal_max_tcode = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_TCODE
self._optimal_min_weight = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_WEIGHT
self._optimal_max_weight = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_WEIGHT
self._optimal_min_gtgweakest = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MIN_GTGWEAKEST
self._optimal_max_gtgweakest = ALIGNEDSTOPCODONGRAPH_OPTIMALITY_MAX_GTGWEAKEST
# run function codingblock_collectionharvesting.align_stop_codons
# to fully initialize the object
self = codingblock_collectionharvesting.align_stop_codons(cbg, self)
def add_edge(self, u, v, wt=1, entropy=1.0):
"""
"""
OrganismGraph.add_edge(self,u,v,wt=wt)
self._edge_binary_entropies[(u,v)] = (entropy,entropy)
self._edge_binary_entropies[(v,u)] = (entropy,entropy)