@deprecated(as_of="0.4.0", until="0.5.0",
            reason="Will be replaced by a SubstitutionMatrix class. To track "
                   "progress, see [#161]"
                   "(https://github.com/biocore/scikit-bio/issues/161).")
def make_identity_substitution_matrix(match_score, mismatch_score,
                                      alphabet='ACGTU'):
    result = {}
    for c1 in alphabet:
        row = {}
        for c2 in alphabet:
            if c1 == c2:
                row[c2] = match_score
            else:
                row[c2] = mismatch_score
        result[c1] = row
    return result


# Functions from here allow for generalized (global or local) alignment. I
# will likely want to put these in a single object to make the naming a little
# less clunky.
Generate substitution matrix where all matches are scored equally
dataset/ETHPy150Open biocore/scikit-bio/skbio/alignment/_pairwise.py/make_identity_substitution_matrix