def layout_chroms(arg, start=None, end=None):
if start is None:
start = arg.start
if end is None:
end = arg.end
tree = arg.get_marginal_tree(start)
arglib.remove_single_lineages(tree)
last_pos = start
blocks = []
leaf_layout = []
layout_func = layout_tree_leaves
#layout_func = layout_tree_leaves_even
for spr in arglib.iter_arg_sprs(arg, start=start, end=end,
use_leaves=True):
print "layout", spr[0]
blocks.append([last_pos, spr[0]])
leaf_layout.append(layout_func(tree))
inorder = dict((n, i) for i, n in enumerate(inorder_tree(tree)))
# determine SPR nodes
rnode = arglib.arg_lca(tree, spr[1][0], spr[0])
cnode = arglib.arg_lca(tree, spr[2][0], spr[0])
# determine best side for adding new sister
left = (inorder[rnode] < inorder[cnode])
# apply spr
arglib.apply_spr(tree, rnode, spr[1][1], cnode, spr[2][1], spr[0])
# adjust sister
rindex = rnode.parents[0].children.index(rnode)
if left and rindex != 0:
rnode.parents[0].children.reverse()
last_pos = spr[0]
blocks.append([last_pos, end])
leaf_layout.append(layout_func(tree))
return blocks, leaf_layout
def layout_chroms(arg, start=None, end=None):
if start is None:
start = arg.start
if end is None:
end = arg.end
tree = arg.get_marginal_tree(start)
arglib.remove_single_lineages(tree)
last_pos = start
blocks = []
leaf_layout = []
layout_func = layout_tree_leaves
#layout_func = layout_tree_leaves_even
for spr in arglib.iter_arg_sprs(arg, start=start, end=end, use_leaves=True):
print "layout", spr[0]
blocks.append([last_pos, spr[0]])
leaf_layout.append(layout_func(tree))
inorder = dict((n, i) for i, n in enumerate(inorder_tree(tree)))
# determine SPR nodes
rnode = arglib.arg_lca(tree, spr[1][0], spr[0])
cnode = arglib.arg_lca(tree, spr[2][0], spr[0])
# determine best side for adding new sister
left = (inorder[rnode] < inorder[cnode])
# apply spr
arglib.apply_spr(tree, rnode, spr[1][1], cnode, spr[2][1], spr[0])
# adjust sister
rindex = rnode.parents[0].children.index(rnode)
if left and rindex != 0:
rnode.parents[0].children.reverse()
last_pos = spr[0]
blocks.append([last_pos, end])
leaf_layout.append(layout_func(tree))
return blocks, leaf_layout