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 0.6.0. Will be replaced by a SubstitutionMatrix class. To track progress, see [#161](https://github.com/biocore/scikit-bio/issues/161).

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:

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.

Return type:

dict of dicts