[RFC]: Add functions guess_parse and guess_alphabet

[jakobnissen]

This PR creates the functions guess_parse and guess_alphabet, which infers an appropriate alphabet for the sequence:

julia> guess_parse("UAUHVCG")
7nt RNA Sequence:
UAUHVCG

julia> guess_parse("LVVWKREFVL")
10aa Amino Acid Sequence:
LVVWKREFVL

Notes for reviewers

• This PR does not implement a good API for recoverable parsing, to be used in libraries. That is, it's not a stab at Add tryparse(::BioSequence, s::AbstractString) or similar #224 . Rather, it's intended for interactive REPL work
• The name could use some bikeshedding! 😄 Ideally, the name
  • Is short. It'll be used in the REPL, after all
  • Makes it clear that this function is a heuristic / loose / guessing function
• Should we have a macro for this? guess"TAGTGCA" or whatever?

Closes #268
Does not close the similar #224

[codecov]

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (1314bbf) 90.89% compared to head (3ae5494) 91.14%.
Report is 1 commits behind head on master.

Files	Patch %	Lines
src/alphabet.jl	94.11%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #292      +/-   ##
==========================================
+ Coverage   90.89%   91.14%   +0.24%     
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  Files          31       31              
  Lines        2395     2416      +21     
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+ Hits         2177     2202      +25     
+ Misses        218      214       -4     

Flag	Coverage Δ
unittests	91.14% <95.65%> (+0.24%)	⬆️

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[kescobo]

In terms of name, if the goal is for easy typing, I think underscores are a no no (for me personally). guess or guessparse seem ok.

I do like guess"AATTCC", but if you're copying a sequence, you probably know if it's aa or dna or whatever - I'd expect to us this more in a loop or something, where the macro form is less useful.

[kescobo]

I dig it! The bit shifting stuff is inscrutable to me, but I like the tests, and the caveats are sufficiently documented IMO

[kescobo]

Meant to approve

[cjprybol]

Like Kevin, I can't say I feel like I'm much help on the bit-code, but the rest of this looks great and I'm very excited about this functionality. I don't know if I'm the only one, but it feels like so few bioinformatics tools do any pre-processing validation of fasta files on their own. The number of hours I've wasted debugging code when someone throws a protein fasta into a collection of DNA fastas and uses .fasta for both instead of .fna & .faa extensions 😅

[jakobnissen]

Thanks for your inputs! I'd like to merge soon.
I'm still a bit torn on the name though. I agree that guess_parse is awkward. But I also don't like that neither the name nor the argument says anything about what it parses into.
Maybe bioseq?