skbio.alignment.make_identity_substitution_matrix¶

skbio.alignment.make_identity_substitution_matrix(match_score, mismatch_score, alphabet='ACGTU')[source]¶

Generate substitution matrix where all matches are scored equally

Note

Deprecated as of 0.4.0 for removal in 0.5.2. Will be replaced by a SubstitutionMatrix class. To track progress, see [#161](https://github.com/biocore/scikit-bio/issues/161).

Parameters:

Parameters:	match_score : int, float The score that should be assigned for all matches. This value is typically positive. mismatch_score : int, float The score that should be assigned for all mismatches. This value is typically negative. alphabet : iterable of str, optional The characters that should be included in the substitution matrix.
Returns:	dict of dicts All characters in alphabet are keys in both dictionaries, so that any pair of characters can be looked up to get their match or mismatch score.

match_score : int, float

The score that should be assigned for all matches. This value is typically positive.

mismatch_score : int, float

The score that should be assigned for all mismatches. This value is typically negative.

alphabet : iterable of str, optional

The characters that should be included in the substitution matrix.

Returns:

dict of dicts

All characters in alphabet are keys in both dictionaries, so that any pair of characters can be looked up to get their match or mismatch score.