tree_type = "nexus"
elif first.find("<") > -1:
tree_type = "phyloxml"
else:
tree_type = "newick"
f.close()
if tree_type == "newick":
# only one tree per file, so get a tree
tree = dendropy.Tree.get_from_path(filename, tree_type)
dpy_trees[tree.label] = tree
dpy_tree_list.append(tree)
else:
# the others can have more than one per,
# so get a TreeList
t = dendropy.TreeList.get_from_path(filename, tree_type)
if not t is None:
for i in t:
dpy_trees[i.label] = i
dpy_tree_list.append(i)
trees = {}
tree_list = []
""" At this point, dpy_trees is full, now we need to convert these dendropy trees to the detangle
trees which are optimized for rotations. Luckily, dendropy trees have a utility function that
provides us with exactly the simple Newick string detangle.tree likes."""
for i in dpy_tree_list:
tr = tree("tree " + i.label + " = [&U] " + i.as_newick_string())
trees[tr.name] = tr
tree_list.append(tr)
process_trees(tree_list, output_filename=args.output_filename)
ct.move_to(x_pos + (branch_length * (max_depth-depth)), y_pos + upper)
ct.line_to(x_pos + (branch_length * (max_depth-depth)), y_pos + lower)
ct.stroke()
if current == tr.root:
return (max_depth+1) * branch_length
else:
return (top, upper + ((lower - upper)/2.00))
if __name__=='__main__':
"""
Loop over all files, reading in all available trees.
"""
for line in fileinput.input():
#line = line.trim()
if line[0:4] == 'tree':
tr = tree(line)
if first_tree == None:
first_tree = tr.name
trees[tr.name] = tr
tree_list.append(tr)
twists[tr.name] = tr.get_twists()
#print trees
combos = list(itertools.combinations(tree_list,2))
f = open('output.svg', 'w')
surf = cairo.SVGSurface(f, len(combos) * (120 + line_gap+ line_region_width) * 2, len(tr.leaves()) * 40)
ct = cairo.Context(surf)
ct.translate(10,16)
ct.set_source_rgb(0.0, 0.0, 0.0)
ct.select_font_face("Georgia", cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
print args
bio_trees = {}
bio_tree_list = []
for filename in args.infiles:
""" Work out what format the file is, then parse the trees out """
f = open(filename, 'r')
first = f.readline()
if first.find('#nexus') > -1 or first.find('#NEXUS') > -1:
tree_type='nexus'
elif first.find('<') > -1:
tree_type='phyloxml'
else:
tree_type='newick'
f.close()
temp = list(Phylo.parse(filename,tree_type))
if not temp is None:
for i in temp:
bio_trees[i.name] = i
bio_tree_list.append(i)
trees = {}
tree_list = [ ]
""" At this point, bio_trees is full, now we need to convert these Phylo trees to the detangle
trees which are optimized for rotations. """
for i in bio_tree_list:
tr = tree()
tr.init_from_phylo(i)
trees[tr.name]=tr
tree_list.append(tr)
process_trees(tree_list, output_filename = args.output_filename)
