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h1newick = "((r5,(r4,(r3,((r2,(r0,r1):4.268188213461936):2.9023407392778653)#H9:10.0::0.7093477022612464):3.2038798063864555):10.0):10.0,r6,(r7,#H9:0.0::0.2906522977387535):10.0);" tree, admix = toytree.utils.parse_network(h1newick)
--------------------------------------------------------------------------- NewickError Traceback (most recent call last) <ipython-input-190-34a9c85f9024> in <module> 1 h1newick = "((r5,(r4,(r3,((r2,(r0,r1):4.268188213461936):2.9023407392778653)#H9:10.0::0.7093477022612464):3.2038798063864555):10.0):10.0,r6,(r7,#H9:0.0::0.2906522977387535):10.0);" ----> 2 tree, admix = toytree.utils.parse_network(h1newick) /moto/eaton/users/pfm2119/pkgs/toytree/toytree/utils.py in parse_network(net, disconnect, root) 156 157 # parse cleaned newick and set empty gamma on all nodes --> 158 net = toytree.tree(net, tree_format=1) 159 160 # store admix data /moto/eaton/users/pfm2119/pkgs/toytree/toytree/Toytree.py in __init__(self, newick, tree_format, **kwargs) 68 # parse a str, URL, or file 69 elif isinstance(newick, (str, bytes)): ---> 70 self.treenode = TreeParser(newick, tree_format).treenodes[0] 71 72 # make an empty tree /moto/eaton/users/pfm2119/pkgs/toytree/toytree/TreeParser.py in __init__(self, intree, tree_format, multitree, debug) 78 # parse intree 79 if not self.debug: ---> 80 self._run() 81 82 /moto/eaton/users/pfm2119/pkgs/toytree/toytree/TreeParser.py in _run(self) 94 95 # parse newick strings to treenodes list ---> 96 self.get_treenodes() 97 98 # apply names from tdict /moto/eaton/users/pfm2119/pkgs/toytree/toytree/TreeParser.py in get_treenodes(self) 162 163 # extract one tree --> 164 self.treenodes.append(extractor.newick_from_string()) 165 166 else: /moto/eaton/users/pfm2119/pkgs/toytree/toytree/TreeParser.py in newick_from_string(self) 265 closing_internal = closing_internal.rstrip(";") 266 # read internal node data and go up one level --> 267 self.apply_node_data(closing_internal, "internal") 268 self.current_parent = self.current_parent.up 269 return self.root /moto/eaton/users/pfm2119/pkgs/toytree/toytree/TreeParser.py in apply_node_data(self, subnw, node_type) 327 self.current_node.add_feature(fname, fvalue) 328 else: --> 329 raise NewickError("Unexpected newick format {}".format(subnw)) 330 331 NewickError: Unexpected newick format #H9:10.0::0.7093477022612464
I will look for what's causing this but wanted to drop it here too in case you're able to beat me to it!
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Occassionally snaq returns a network that toytree cannot parse. Here's an example of something that gives an error:
Full error text:
I will look for what's causing this but wanted to drop it here too in case you're able to beat me to it!
The text was updated successfully, but these errors were encountered: