add Sequence.replace

[gregcaporaso]

This should likely take a boolean vector and a character to assign to all sequence positions corresponding to True values in the boolean vector. This would be useful, for example, for replacing all gap characters with the default gap character, or all degenerate characters with a single degenerate character (likely N).

[ebolyen]

Depending on how people feel, we could also support both of these statements:

with sequence.replace(mutate=True) as raw:
    raw[[3, 2, 1]] = [b'A', b'C', b'T']

and

sequence.replace([3, 2, 1], 'N')

[jairideout]

👎 for the first example. I think sequence data should remain immutable unless we have a real need for mutability. If we want to support mutability, the __setitem__ API is likely more intuitive for users:

sequence[[3, 2, 1]] = [b'A', b'C', b'T']

[ebolyen]

Good point