Caio Fontes

You made two changes in your examples, not only you changed from `super()` to `Residue` but you also started passing the args to the `__init__()` method. I suspect the arg...

I didn't encounter this error in my tests, will fix in the next few days and request the review, sorry for opening the PR before it was ready.

> I personally like the inclusion of type annotation, any thoughts on how we can validate it / use it in the test suite? See also #3165 @peterjc do you...

> Yes, I was hoping you were familiar enough with mypy that you'd at least be able to suggest the key commands to run, even if one of us has...

Any other changes necessary here?

@peterjc without the type annotations do you think this can be merged? Can remove them to avoid dealing with inconsistencies in the library

Will reimplement `count_kmers` taking your comments into account, will also drop `Counter` in favor of `str.count` due to performance reasons, mistakenly thought they would be equivalent.

> For consistency with the other parsers, you need to return handle an empty file a little differently: > > ``` > ====================================================================== > ERROR: test_empty_file (test_SeqIO.TestSeqIO) > Check parsers...

I agree with the use of the word fraction instead of ratio, I maintained mainly because it was in the first PR, and since that word choice was apparently approved...

Will start to work on the proposed changes with the `ignore_ambiguous=True` keyword. Just so I'm not confused, the expected behavior in the following cases (in a format similar to what...