Question: ETE3: error while parsing Newick tree
0
gravatar for a.zielezinski
8 months ago by
a.zielezinski9.2k
a.zielezinski9.2k wrote:

Any idea why ETE Toolkit (ete3) throws an error while parsing the following Newick tree:

((((A,B),C),(((D,E),F),(((((G,H),I),J),K),L)))(M,N));

from ete3 import Tree
s = '((((A,B),C),(((D,E),F),(((((G,H),I),J),K),L)))(M,N));'
t = Tree(s)

The error message:

ete3.parser.newick.NewickError: Broken newick structure at: G,H),I),J),K),L)))
You may want to check other newick loading flags like 'format' or 'quoted_node_names'.

I also tried loading the tree with all the format flag (and values from 0 to 9).

ete tree newick ete3 • 251 views
ADD COMMENTlink modified 8 months ago by Mensur Dlakic5.8k • written 8 months ago by a.zielezinski9.2k
3
gravatar for Mensur Dlakic
8 months ago by
Mensur Dlakic5.8k
USA
Mensur Dlakic5.8k wrote:

You need comma between L))) and (M,N).

ADD COMMENTlink written 8 months ago by Mensur Dlakic5.8k
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