grabear · April 21, 2017 19:21 · Jun 23, 2015 · Feb 25, 2014
diff --git a/gistfile1.py → Newick2JSON.py b/gistfile1.py → Newick2JSON.py
diff --git a/gistfile1.py b/gistfile1.py
@@ -0,0 +1,43 @@
+import sys
+from ete2 import Tree
+import random
+
+def get_json(node):
+    # Read ETE tag for duplication or speciation events
+    if not hasattr(node, 'evoltype'):
+        dup = random.sample(['N','Y'], 1)[0]
+    elif node.evoltype == "S":
+        dup = "N"
+    elif node.evoltype == "D":
+        dup = "Y"
+
+    node.name = node.name.replace("'", '')
+
+    json = { "name": node.name, 
+             "display_label": node.name,
+             "duplication": dup,
+             "branch_length": str(node.dist),
+             "common_name": node.name,
+             "seq_length": 0,
+             "type": "node" if node.children else "leaf",
+             "uniprot_name": "Unknown",
+             }
+    if node.children:
+        json["children"] = []
+        for ch in node.children:
+            json["children"].append(get_json(ch))
+    return json
+
+
+if __name__ == '__main__':
+    if len(sys.argv) > 1:
+        t = Tree(sys.argv[1])
+
+    else:
+        # create a random example tree
+        t = Tree()
+
+        t.populate(100, random_branches=True)
+
+    # TreeWidget seems to fail with simple quotes
+    print str(get_json(t)).replace("'", '"')