def ExonCollectionGraph2AcceptorSiteCollectionGraph(gra):
"""
Convert ECG -> AcceptorSiteCollectionGraph
@attention: only in use when ECG is NOT a FirstExon ECG
@rtype: AcceptorSiteCollectionGraph
@return: AcceptorSiteCollectionGraph instance to be placed in the CBG
"""
newgra = AcceptorSiteCollectionGraph()
newgra.ALIGNED_SITE_AA_OFFSET = 10
newgra.MIN_PSSM_SCORE = -0.0
for node in gra.get_nodes():
accep = gra._node_object[node].acceptor
if accep.__class__.__name__ == 'CodingBlockStart':
phase = gra.acceptor_phase()
# return a ProjectedSpliceSite
projAccep = CodingBlockStart2ProjectedSpliceAcceptor(accep,phase=phase)
newnode = ( node[0], node[1], projAccep.pos )
newgra.add_node_and_object(newnode,projAccep)
newgra._node_pssm[newnode] = accep.pssm_score
else:
newnode = ( node[0], node[1], accep.pos )
newgra.add_node_and_object(newnode,accep)
newgra._node_pssm[newnode] = accep.pssm_score
for nodeA,nodeB in newgra.pairwisecrosscombinations_node():
entropyQ = 1.0
entropyS = 1.0
newgra.add_edge(nodeA,nodeB,wt=1.0)
newgra._edge_binary_entropies[(nodeA,nodeB)] = (entropyQ,entropyS)
newgra._edge_binary_entropies[(nodeB,nodeA)] = (entropyS,entropyQ)
return newgra
