`--brlen` does not accept "fix" as an argument

jbloomlab / phydms

phylogenetic analyses informed by deep mutational scanning data

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`--brlen` does not accept "fix" as an argument #8

Closed skhilton closed 7 years ago

skhilton commented 7 years ago

command: phydms NP_data/NP_alignment.fasta NP_data/NP_tree.newick YNGKP_M0 testOut/ --brlen fix

The data is the NP data in the tests directory.

error:

File "/Users/sarah/Library/Python/3.5/lib/python/site-packages/phydms-2.0.dev0-py3.5-macosx-10.6-intel.egg/EGG-INFO/scripts/phydms", line 223, in main
    raise ValueError("Invalid brlen {0}".format(args['brlen']))
ValueError: Invalid brlen fix

jbloom commented 7 years ago

This is expected. I have removed the fix option for --brlen. The only two allowed options should now be optimize and scale. That's because it doesn't really make sense to fix the branch lengths -- we always want to at least scale them.