def simData_XExtraMutations(N,L,k,mutationsMustBeVisible =True):
simTree = simulator_KingmanFiniteSites(N,10*L/2.0,L,False)
result = simTree.untillFirstXInconsistencies(X = k)
if not mutationsMustBeVisible:
# assure that we have k more mutations on the underlying tree than
# we have segregating sites
while result["Inconsistencies"] < k:
result = simTree.untillFirstXInconsistencies(X = k)
else:
# Assure that we have k visible inconsistencies with the infinite sites
# model
while result["typeCount"][0] + result["typeCount"][2] < k:
result = simTree.untillFirstXInconsistencies(X = k)
S_redundantRowsAndColumns = simTree.getS()
#remove null-rows
S1 = withoutNullColumns(S_redundantRowsAndColumns)
#remove redundant rows, and associate each row with a count-vector n instead
S,n = S_and_n(S1)
return S,n
def simData_k_mutations_total(N,L,k,mutation_must_be_visible = True):
simTree = simulator_KingmanFiniteSites(N,10.0*k,L,False)
if mutation_must_be_visible:
result = simTree.until_k_visible_mutations(k)
else:
result = simTree.until_k_mutations(k)
#re-run simulations if we didn't get enough mutations.
while k > len(result['coalescent'].mutations):
simTree = simulator_KingmanFiniteSites(N,10.0*k,L,False)
if mutation_must_be_visible:
result = simTree.until_k_visible_mutations(k)
else:
result = simTree.until_k_mutations(k)
S_redundant_rows_and_columns = result['S']
S_redundant_columns, Nr = S_and_n( S_redundant_rows_and_columns )
S_transpose, Nc = S_and_n( np.transpose(S_redundant_columns) )
S = np.transpose(S_transpose)
return S,Nr,Nc
def simData(N,theta,L):
simTree = simulator_KingmanFiniteSites(N,theta/2,L)
S_redundantRowsAndColumns = simTree.getS()
#remove null-rows
S1 = withoutNullColumns(S_redundantRowsAndColumns)
#remove redundant rows, and associate each row with a count-vector n instead
S,n = S_and_n(S1)
return S,n
def test(n = 10, theta = 1.0, L = 10):
sim = fsmi.simulator_KingmanFiniteSites(n,theta,L)
myTree = sim_to_tree(sim)
# str_newick_test = '(A,(B,C)D);'
# dpTree_test = dp.Tree.get(data = str_newick_test, schema = 'newick')
# dpTree_test.print_plot()
str_newick_sim = myTree.str_newick(True)
print str_newick_sim
dpTree_sim = dp.Tree.get(data = str_newick_sim, schema = 'newick')
dpTree_sim.print_plot()
phyloTree = Phylo.read(StringIO(str_newick_sim),'newick')
print phyloTree
plt.figure()
Phylo.draw(phyloTree)
phyloTree.rooted = True
plt.figure()
Phylo.draw_graphviz(phyloTree, prog = 'dot')
plt.draw()
