tree: Unable to use IQ-TREE -g option if strain name contains certain characters

[joverlee521]

Current Behavior

Within augur tree we replace certain characters in strain names with random strings before passing the renamed FASTA to IQ-TREE.

augur/augur/tree.py

Lines 214 to 219 in 945b49a

	def random_string(n):
	from string import ascii_uppercase as letters
	return "".join([letters[i] for i in np.random.randint(len(letters), size=n)])
	prefix = "DELIM"
	escape_dict = {c:f'_{prefix}-{random_string(20)}_' for c in '/|()*'}
	reverse_escape_dict = {v:k for k,v in escape_dict.items()}

This results in IQ-TREE being unable to match the original strain names provided in the constraint tree via the -g option.

Expected behavior

I'm not sure what should be the expected behavior here. Do we want to be able to support all IQ-TREE options via augur tree or do we make it clear that certain options may not work?

Additional context

First noticed this issue when exploring nextstrain/seasonal-flu#79 with @corneliusroemer

[victorlin]

Do we want to be able to support all IQ-TREE options via augur tree or do we make it clear that certain options may not work?

No, we should update docs to make this clear.