def test_read_write(self):
"""Read and write an ARG"""
rho = 1.5e-8 # recomb/site/gen
l = 10000 # length of locus
k = 10 # number of lineages
n = 2*10000 # effective popsize
arg = arglib.sample_arg(k, n, rho, 0, l)
# round ages and pos for easy equality
for node in arg:
node.age = round(node.age)
node.pos = round(node.pos)
stream = StringIO.StringIO()
arglib.write_arg(stream, arg)
stream.seek(0)
arg2 = arglib.read_arg(stream)
self.assertTrue(arg.equal(arg2))
def test_recomb(self):
"""
Investigate the fact that some recombinations are not visible
"""
k = 3
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8
length = 1000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
times = arghmm.get_time_points(10)
arghmm.discretize_arg(arg, times)
arg.set_ancestral()
arg.prune()
recombs = arglib.get_recomb_pos(arg)
# find recombs by walking
recombs2 = []
i = 0
while True:
tree = arg.get_marginal_tree(i - .5)
recomb = arghmm.find_tree_next_recomb(tree, i + 1, tree=True)
if recomb:
recombs2.append(recomb.pos)
i = recomb.pos
else:
break
# these are suppose to differ because some recombination occur
# in the hole of ancestral sequence intervals
print recombs
print recombs2
arglib.write_arg("tmp/b.arg", arg)
def test_recomb(self):
"""
Investigate the fact that some recombinations are not visible
"""
k = 3
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8
length = 1000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
times = arghmm.get_time_points(10)
arghmm.discretize_arg(arg, times)
arg.set_ancestral()
arg.prune()
recombs = arglib.get_recomb_pos(arg)
# find recombs by walking
recombs2 = []
i = 0
while True:
tree = arg.get_marginal_tree(i-.5)
recomb = arghmm.find_tree_next_recomb(tree, i+1, tree=True)
if recomb:
recombs2.append(recomb.pos)
i = recomb.pos
else:
break
# these are suppose to differ because some recombination occur
# in the hole of ancestral sequence intervals
print recombs
print recombs2
arglib.write_arg("tmp/b.arg", arg)
move_layout(layout1, x=i*(nleaves+2))
move_layout(layout2, x=(i+1)*(nleaves+2))
mapping = get_mapping(tree1, tree2, pos, times)
draw_mapping(tree1, tree2, layout1, layout2, times, mapping)
#=============================================================================
if 0:
k = 10
n = 1e4
rho = 1.5e-8 * 100
mu = 2.5e-8
length = 1000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
arglib.write_arg("tmp/a.arg", arg)
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
#arg = arglib.read_arg("tmp/a.arg")
#arg.set_ancestral()
#find_recomb_coal(tree, last_tree, recomb_name=None, pos=None)
times = arghmm.get_time_points(30, maxtime=60e3)
arghmm.discretize_arg(arg, times)
# get recombs
recombs = list(x.pos for x in arghmm.iter_visible_recombs(arg))
print "recomb", recombs
pos = recombs[0] + 1
# treelib.layout_tree(tree2, xscale=1, yscale=1), leaves=0)
move_layout(layout1, x=i * (nleaves + 2))
move_layout(layout2, x=(i + 1) * (nleaves + 2))
mapping = get_mapping(tree1, tree2, pos, times)
draw_mapping(tree1, tree2, layout1, layout2, times, mapping)
#=============================================================================
if 0:
k = 10
n = 1e4
rho = 1.5e-8 * 100
mu = 2.5e-8
length = 1000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
arglib.write_arg("tmp/a.arg", arg)
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
#arg = arglib.read_arg("tmp/a.arg")
#arg.set_ancestral()
#find_recomb_coal(tree, last_tree, recomb_name=None, pos=None)
times = arghmm.get_time_points(30, maxtime=60e3)
arghmm.discretize_arg(arg, times)
# get recombs
recombs = list(x.pos for x in arghmm.iter_visible_recombs(arg))
print "recomb", recombs
pos = recombs[0] + 1