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FePhyFoFum / phyx

phylogenetics tools for linux (and other mostly posix compliant) computers
blackrim.org
GNU General Public License v3.0
111 stars 17 forks source link

pxs2nex should make Nexus-compliant sequence names #153

Closed josephwb closed 3 years ago

josephwb commented 3 years ago

Things like space confuse things e.g. PAUP* thinks a space separates the name and the sequence.

Either 1) substitute '_' for ' ', or 2) quote strings.

josephwb commented 3 years ago

Some smart person already wrote the code to do this here.

josephwb commented 3 years ago

Hrm it is already using it? Maybe my test data are bad...

josephwb commented 3 years ago

Fixed with fbfef0d. Went with get_valid_nexus_label() rather than what was being used (get_safe_taxon_label()), as the latter does substitution, which could break matching across files.