Open ArtPoon opened 9 years ago
from NewickIO.py:
elif token == ')':
# done adding children for this parent clade
parent = self.process_clade(current_clade)
if not parent:
raise NewickError('Parenthesis mismatch.')
So script is encountering a tree string with an unmatched closing parenthesis.
This bug has a very low rate of occurrence. I am going to catch this exception in kamphir.py, simulate() by "manually" iterating over the file of Newick strings and passing the rare case where the string is mangled. The rest of the parsed trees will be returned as a List object. Eventually it would be nice to chase this one, but for now I'm closing with commit.
Captured a couple of trees that raised this exception, saved as crash.tree
and crash2.tree
.