added STDR wrap-around #94
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richardyz98
commented
May 13, 2021
cassiopeia/solver/STDRSolver.py
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| min_split = 1, | ||
| merge_method = "least_square", | ||
| verbose=False) | ||
| tree = data_utilities.ete3_to_networkx(ete3.Tree(tree_stdr_nj.as_string(schema="newick"))) |
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The reason that I'm using ete3 here instead of inputting the string directly into populate_tree is because the formatting is off. Right now, populate_tree and newick_to_network both assume a specific newick format, specifically those with internal nodes in the newick string. Should I add an argument to newick_to_network, populate_tree, and the init of CassiopeiaTree allowing for the user to specify the newick format?
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Hi Matt, here's what I have for the STDR wrap-around currently. It's not thoroughly documented, so I'll work on that.