PFM for amino acid sequences?

[fcharih]

I noticed that the PFM function does not run on protein sequences. Is there a biological rationale for this or is this simply missing functionality?

pfm_matrix
ArgumentError: sequence element must be DNA or RNA

BioSequences.PFM(::Array{BioSequences.LongSequence{BioSequences.AminoAcidAlphabet},1})@pwm.jl:52
top-level scope@Local: 1[inlined]

[jakobnissen]

As far as I can tell, the PFM/PWM functionality has not been used much.
The functionality has been updated with three commits: The initial back in 2017, and once for v 1.0 and v2.0. It's probably a relic from older times, and I think it belongs in a separate package. Might be worth removing for v3.0

But anyway yeah, it looks to me like it could be implemented with arbitrary alphabets, not just DNA/RNA. It also looks like it handles ambiguous nucleotides a little strangely, too.

A PR would be much welcome! :)