Add two new utilities

OZprivate/ServerScripts/Utilities/format_newick.py

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+#!/usr/bin/env python3
+'''
+Format a newick tree with indentation to make it more human readable. This is not meant for very large trees.
+
+For example, if the input tree is:
+
+(Tupaia_tana:8.5,(Tupaia_picta:8.0,(Tupaia_montana:7.0,Tupaia_splendidula:7.0):1.0):0.5):4.5;
+
+The output is:
+
+(
+  Tupaia_tana:8.5,
+  (
+    Tupaia_picta:8.0,
+    (
+      Tupaia_montana:7.0,
+      Tupaia_splendidula:7.0
+    ):1.0
+  ):0.5
+):4.5;
+'''
+
+import argparse
+import sys
+from dendropy import Tree
+
+parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+parser.add_argument('treefile', type=argparse.FileType('r'), nargs='?', default=sys.stdin, help='The tree file in newick form')
+parser.add_argument('outfile', type=argparse.FileType('w'), nargs='?', default=sys.stdout, help='The output tree file')
+parser.add_argument('--indent_spaces', '-i', default=2, type=int, help='the number of spaces for each indentation level')
+args = parser.parse_args()
+
+tree = Tree.get(stream=args.treefile, schema='newick', preserve_underscores=True, suppress_leaf_node_taxa=True, suppress_internal_node_taxa=True)
+output_stream = args.outfile
+indent_string = ' ' * args.indent_spaces
+
+def process_node(node, depth):
+    output_stream.write(indent_string * depth)
+
+    if len(node.child_nodes()) > 0:
+        output_stream.write('(\n')
+
+        # Go through children and process them recursively, increasing the depth
+        for count, child_node in enumerate(node.child_nodes()):
+            process_node(child_node, depth+1)
+
+            # Commas between the children
+            if count < len(node.child_nodes())-1:
+                output_stream.write(',')
+
+            output_stream.write('\n')
+
+        output_stream.write(indent_string * depth + ')')
+
+    if node.label:
+        output_stream.write(node.label)
+    if node.edge_length:
+        output_stream.write(':' + str(node.edge_length))
+
+process_node(tree.seed_node, 0)
+
+# Need a ; at the end of the newick
+output_stream.write(';\n')

OZprivate/ServerScripts/Utilities/ultrametric_to_additive.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+'''
+Transform an ultrametric newick tree into an additive newick tree
+
+e.g. if A split from B 7 MYA, and C split from A&B 20 MYA, the ultrametric tree would be:
+
+(
+  (
+    A,
+    B
+  ):7,
+  C
+):20;
+
+And this code turns that into a proper additive newick tree:
+
+(
+  (
+    A:7,
+    B:7
+  ):13,
+  C:20
+);
+
+Note that the input is a clear abuse of the newick branch length syntax, since
+we're not actually storing length, but ages. It is however convenient as a
+transitional format when translating an ultrametric diagram to newick format.
+'''
+
+import argparse
+import sys
+from dendropy import Tree
+
+parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+parser.add_argument('treefile', type=argparse.FileType('r'), nargs='?', default=sys.stdin, help='The ultrametric tree in newick form')
+parser.add_argument('outfile', type=argparse.FileType('w'), nargs='?', default=sys.stdout, help='The output newick tree file')
+args = parser.parse_args()
+
+def process_node(node, parent_age):
+    # If a input node has a length, it's semantically an age, not a length
+    node_age = node.edge_length if node.edge_length else 0
+
+    # The actual edge length is the difference between the parent age and the node age
+    node.edge_length = round(parent_age - node_age, 2)
+    if node.edge_length == 0:
+        node.edge_length = None 
+
+    # Process children recursively, 
+    for child_node in node.child_nodes():
+        process_node(child_node, node_age)
+
+tree = Tree.get(stream=args.treefile, schema='newick', preserve_underscores=True,
+    suppress_leaf_node_taxa=True, suppress_internal_node_taxa=True)
+process_node(tree.seed_node, tree.seed_node.edge_length if tree.seed_node.edge_length else 0)
+
+tree.write(file=args.outfile, schema='newick', suppress_leaf_node_labels=False) 
+