Patterns from MSA function

[LinguList]

This function is always needed again and again, one might want to just add it to util:

from lingpy.sequence.sound_classes import token2class

def patterns_from_msa(msa, languages, missing="Ø", gap="-"):
    """
    Retrieve patterns from an msa object.
    """
    out = [["" for x in languages] for y in msa["alignment"][0]]
    for j in range(len(msa["alignment"][0])):
        for i, language in enumerate(languages):
            if language in msa["taxa"]:
                out[j][i] = msa["alignment"][msa["taxa"].index(language)][j]
            else:
                out[j][i] = missing
    return [(
        token2class(
            ([c for c in row if c not in (gap, missing)] or ["?"])[0], 
            "cv"
            ).lower(),
        tuple(row)) for row in out
            ]

The function takes an MSA object and returns the patterns. One can also do it without the structure involved, or one could do it passing the structure, as done in lingrex.