def test_sample_birth_times(self):
stree = read_tree("test/data/flies.stree")
birth = 8.1
death = 2.1 * 1.0001
print spidir.birthDeathCount(4, .005, birth, death)
print spidir.birthDeathCounts(1, 4, .005, birth, death)
maxgenes = [5, 10, 20, 40, 50]
tic("time")
counts = [2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 2]
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree,
counts,
birth,
death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
toc()
counts = [1] * 12
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree,
counts,
birth,
death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
counts = [4] * 12
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree,
counts,
birth,
death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
def test_sample_birth_rates(self):
prep_dir("test/output/birth_death_est")
stree = read_tree("test/data/flies.stree")
maxgene = 20
counts = [2, 2, 3, 3, 3, 2, 0, 0, 0, 3, 3, 2]
#counts = [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
rates = list(frange(.1, 20, 1))
top = -INF
x = []
y = []
z = []
for birth in rates:
for death in rates:
l = spidir.birth_death_tree_counts(stree,
counts,
birth,
death,
maxgene=maxgene,
rootgene=1)
x.append(birth)
y.append(death)
z.append(l)
if l > top:
top = l
b = birth
d = death
print birth, death, l
print "best:", b, d, top
write_delim("test/output/birth_death_est/rates.txt", zip(x, y, z))
mat = [
mget(z, range(ind, ind + len(rates)))
for ind in xrange(0, len(z), len(rates))
]
#mat = map2(log, mat)
heatmap(mat,
rlabels=map(str, rates),
clabels=map(str, rates),
display=True,
xmargin=100,
ymargin=100)
def test_sample_birth_times(self):
stree = read_tree("test/data/flies.stree")
birth = 8.1
death = 2.1 * 1.0001
print spidir.birthDeathCount(4, .005, birth, death)
print spidir.birthDeathCounts(1, 4, .005, birth, death)
maxgenes = [5, 10, 20, 40, 50]
tic("time")
counts = [2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 2]
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree, counts,
birth, death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
toc()
counts = [1] * 12
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree, counts,
birth, death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
counts = [4] * 12
for maxgene in maxgenes:
logl = spidir.birth_death_tree_counts(stree, counts,
birth, death,
maxgene=maxgene,
rootgene=1)
print maxgene, logl
def test_sample_birth_rates(self):
prep_dir("test/output/birth_death_est")
stree = read_tree("test/data/flies.stree")
maxgene = 20
counts = [2, 2, 3, 3, 3, 2, 0, 0, 0, 3, 3, 2]
#counts = [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
rates = list(frange(.1, 20, 1))
top = -INF
x = []
y = []
z = []
for birth in rates:
for death in rates:
l = spidir.birth_death_tree_counts(stree, counts,
birth, death,
maxgene=maxgene,
rootgene=1)
x.append(birth)
y.append(death)
z.append(l)
if l > top:
top = l
b = birth
d = death
print birth, death, l
print "best:", b, d, top
write_delim("test/output/birth_death_est/rates.txt", zip(x, y, z))
mat = [mget(z, range(ind, ind+len(rates)))
for ind in xrange(0, len(z), len(rates))]
#mat = map2(log, mat)
heatmap(mat, rlabels=map(str, rates), clabels=map(str, rates),
display=True, xmargin=100, ymargin=100)