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Converts a newick file into JSON format for d3/TreeWidget javascript component
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("'", '"')
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