Open jakobnissen opened 11 months ago
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Comparison is base (
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) 91.14%. Report is 1 commits behind head on master.
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src/alphabet.jl | 94.11% | 1 Missing :warning: |
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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.
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 😅
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
?
This PR creates the functions
guess_parse
andguess_alphabet
, which infers an appropriate alphabet for the sequence:Notes for reviewers
guess"TAGTGCA"
or whatever?Closes #268 Does not close the similar #224