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fixup of python recipe #659

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Merged
bhaller merged 2 commits into from
Aug 15, 2026
Merged

fixup of python recipe #659

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1a1214a
fixup of python recipe
petrelharp Aug 14, 2026
d6def05
bug fixup
petrelharp Aug 15, 2026
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24 changes: 13 additions & 11 deletions .../recipes/Recipe 18.10 - Adding a neutral burn-in after simulation with recapitation II.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,23 +9,23 @@

# Calculate tree heights, giving uncoalesced sites the maximum time
def tree_heights(ts):
uncoalesced_height = ts.metadata['SLiM']['tick']
heights = np.zeros(ts.num_trees + 1)
for tree in ts.trees():
if tree.num_roots > 1: # not fully coalesced
heights[tree.index] = uncoalesced_height
else:
children = tree.children(tree.root)
real_root = tree.root if len(children) > 1 else children[0]
heights[tree.index] = tree.time(real_root)
roots = tree.roots
if len(roots) == 1:
children = tree.children(roots[0])
if len(children) == 1:
roots = children
root_heights = [tree.time(r) for r in roots]
assert len(set(root_heights)) == 1
heights[tree.index] = root_heights[0]
heights[-1] = heights[-2] # repeat the last entry for plotting with step
return heights

# Plot tree heights before recapitation
breakpoints = list(ts.breakpoints())
heights = tree_heights(ts)
plt.step(breakpoints, heights, where='post')
plt.show()
plt.step(breakpoints, heights, where='post', label="SLiM")

# Recapitate!
recap = pyslim.recapitate(ts, ancestral_Ne=1e5, recombination_rate=3e-10, random_seed=1)
Expand All @@ -34,7 +34,9 @@ def tree_heights(ts):
# Plot the tree heights after recapitation
breakpoints = list(recap.breakpoints())
heights = tree_heights(recap)
plt.step(breakpoints, heights, where='post')
plt.show()
plt.step(breakpoints, heights, where='post', label="recapitated")
plt.xlabel("genome"); plt.ylabel("time ago (generations)")
plt.savefig("tree_heights.png")



24 changes: 13 additions & 11 deletions .../Recipes/Recipe 18.10 - Adding a neutral burn-in after simulation with recapitation II.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,23 +9,23 @@

# Calculate tree heights, giving uncoalesced sites the maximum time
def tree_heights(ts):
uncoalesced_height = ts.metadata['SLiM']['tick']
heights = np.zeros(ts.num_trees + 1)
for tree in ts.trees():
if tree.num_roots > 1: # not fully coalesced
heights[tree.index] = uncoalesced_height
else:
children = tree.children(tree.root)
real_root = tree.root if len(children) > 1 else children[0]
heights[tree.index] = tree.time(real_root)
roots = tree.roots
if len(roots) == 1:
children = tree.children(roots[0])
if len(children) == 1:
roots = children
root_heights = [tree.time(r) for r in roots]
assert len(set(root_heights)) == 1
heights[tree.index] = root_heights[0]
heights[-1] = heights[-2] # repeat the last entry for plotting with step
return heights

# Plot tree heights before recapitation
breakpoints = list(ts.breakpoints())
heights = tree_heights(ts)
plt.step(breakpoints, heights, where='post')
plt.show()
plt.step(breakpoints, heights, where='post', label="SLiM")

# Recapitate!
recap = pyslim.recapitate(ts, ancestral_Ne=1e5, recombination_rate=3e-10, random_seed=1)
Expand All @@ -34,7 +34,9 @@ def tree_heights(ts):
# Plot the tree heights after recapitation
breakpoints = list(recap.breakpoints())
heights = tree_heights(recap)
plt.step(breakpoints, heights, where='post')
plt.show()
plt.step(breakpoints, heights, where='post', label="recapitated")
plt.xlabel("genome"); plt.ylabel("time ago (generations)")
plt.savefig("tree_heights.png")



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