def extract_clades(newick_file, processed_newick_out=None):
""" the outer logic for tree splitting """
# preprocess tree
print("Pre-processing tree ({})".format(newick_file))
tree = PhyloTree(newick_file)
R = tree.get_midpoint_outgroup()
tree.set_outgroup(R)
tree.ladderize()
tree.convert_to_ultrametric()
if (processed_newick_out is not None):
tree.write(format=1, outfile=processed_newick_out)
# calculate clades
print("Calling clades ({})".format(newick_file))
def get_branch_length(node):
for l in node:
return l.get_distance(node)
len_tree = len(tree)
dist_tree = get_branch_length(tree)
def condition_discard(node, tree):
return (len(node) < 3)
def condition_ok(node, tree):
return len(node) < max(10, len_tree / 50)
branches = get_pruned_branch(tree, tree, condition_discard, condition_ok,
[])
clades = {}
for i, branch in enumerate(
sorted(branches, key=lambda nodes: -1 * len(nodes))):
clades[str(i + 1)] = [node.name for node in branch]
return clades
def main(args):
if args.alignment:
t = PhyloTree(args.tree, alignment=args.alignment, alg_format='fasta')
else:
t = PhyloTree(args.tree)
if args.highlight_new:
runs = read_runs(args.highlight_new)
t.set_outgroup('EM_079422')
t.ladderize()
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_support = False
ts.layout_fn = layout
thick_hz_line = NodeStyle()
thick_hz_line["hz_line_width"] = 8
t.set_style(thick_hz_line)
#t.children[0].set_style(thick_hz_line)
#t.children[1].set_style(thick_hz_line)
thick_vt_line = NodeStyle()
thick_vt_line["vt_line_width"] = 4
t.set_style(thick_vt_line)
# header
if not args.hide_annotations:
ts.aligned_header.add_face(MyTextFace('Sample identifier', fstyle='Bold', fsize=8, tight_text=False), column = 1)
ts.aligned_header.add_face(MyTextFace('Prefecture', fstyle='Bold', fsize=8, tight_text=False), column = 2)
ts.aligned_header.add_face(MyTextFace('Sous-prefecture', fstyle='Bold', fsize=8, tight_text=False), column = 3)
ts.aligned_header.add_face(MyTextFace('Village', fstyle='Bold', fsize=8, tight_text=False), column = 4)
ts.aligned_header.add_face(MyTextFace('Sample received', fstyle='Bold', fsize=8, tight_text=False), column = 5)
if args.positions:
positions = read_positions(args.positions)
alg_header = RulerFace(positions,
col_width=11,
height=0, # set to 0 if dont want to use values
kind="stick",
hlines = [0],
hlines_col = ["white"], # trick to hide hz line
)
ts.aligned_header.add_face(alg_header, 6)
#legend
if args.legend:
legend = {}
for s in samples.values():
legend[s['prefec']] = s['prefec__colour']
for p in sorted(legend.keys()):
ts.legend.add_face(CircleFace(4, legend[p]), column=0)
ts.legend.add_face(MyTextFace(p, fsize=6, tight_text=False), column=1)
ts.legend_position=1
if args.circular:
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 180
# t.show(tree_style=ts)
t.render(args.output, tree_style=ts, w=1024)
def main(args):
if args.alignment:
t = PhyloTree(args.tree, alignment=args.alignment, alg_format='fasta')
else:
t = PhyloTree(args.tree)
if args.highlight_new:
runs = read_runs(args.highlight_new)
t.set_outgroup('EM_079422')
t.ladderize()
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_support = False
ts.layout_fn = layout
thick_hz_line = NodeStyle()
thick_hz_line["hz_line_width"] = 8
t.set_style(thick_hz_line)
#t.children[0].set_style(thick_hz_line)
#t.children[1].set_style(thick_hz_line)
thick_vt_line = NodeStyle()
thick_vt_line["vt_line_width"] = 4
t.set_style(thick_vt_line)
# header
if not args.hide_annotations:
ts.aligned_header.add_face(MyTextFace('Sample identifier', fstyle='Bold', fsize=8, tight_text=False), column = 1)
ts.aligned_header.add_face(MyTextFace('Prefecture', fstyle='Bold', fsize=8, tight_text=False), column = 2)
ts.aligned_header.add_face(MyTextFace('Sous-prefecture', fstyle='Bold', fsize=8, tight_text=False), column = 3)
ts.aligned_header.add_face(MyTextFace('Village', fstyle='Bold', fsize=8, tight_text=False), column = 4)
ts.aligned_header.add_face(MyTextFace('Sample received', fstyle='Bold', fsize=8, tight_text=False), column = 5)
if args.positions:
positions = read_positions(args.positions)
alg_header = RulerFace(positions,
col_width=11,
height=0, # set to 0 if dont want to use values
kind="stick",
hlines = [0],
hlines_col = ["white"], # trick to hide hz line
)
ts.aligned_header.add_face(alg_header, 6)
#legend
if args.legend:
legend = {}
for s in list(samples.values()):
legend[s['prefec']] = s['prefec__colour']
for p in sorted(legend.keys()):
ts.legend.add_face(CircleFace(4, legend[p]), column=0)
ts.legend.add_face(MyTextFace(p, fsize=6, tight_text=False), column=1)
ts.legend_position=1
if args.circular:
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 180
# t.show(tree_style=ts)
t.render(args.output, tree_style=ts, w=1024)
