skbio.sequence.GrammaredSequence.to_definites#

GrammaredSequence.to_definites(degenerate='wild', noncanonical=True)[source]#

Convert degenerate and noncanonical characters to alternative characters.

Parameters:

degenerate{“wild”, “gap”, “del”, str of length 1}, optional: How degenerate/non-canonical characters should be treated: Replace them with the wildcard character (“wild”, default), or the default gap character (“gap”), or a user-defined character (str of length 1), or remove them (“del”).
noncanonicalbool, optional: Treat non-canonical characters in the same way as degenerate characters (True, default), or leave them as-is (False).

Returns: