add predicate method and tests

[camilogarciabotero]

Adds the new hasprematurestop method

Hi,

This is a simple new method that looks into a BioSequence{<:NucleicAcidAlphabet} and check if there is a premature stop codon. It only happens to run when there is an actual stop codon in the sequence, otherwise throws a MethodError with the corresponding message that no stop codon at the end. It has three test cases, I think they could cover all the instances.

I'm open to comments. This is my first PR in this GH organization and hope the actual method is useful. I have used in one of my packages, but I think it could actually be nice if others get this functionality out from the BioSequences package.

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• [ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
• [ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).

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[jakobnissen]

Thank you for your contribution.

I think the functionality in this PR is too application-specific and somewhat too idiosyncratic to belong in BioSequences. What I mean is that this function allows you to do a very specific query, that is probably not of broad usefulness. The implementation had be asking questions like:

• Why must there be a stop codon at the end? Wouldn't it be useful to have very similar functionality for checking if an ORF has any stop codons at all?
• What about different genetic codes, e.g. the human mitochondrial one?
• Why can't this function search for stop codons from the middle of a sequence, or from any arbitrary positions? That would be very useful when scanning for ORFs.

Me having these questions doesn't mean it's bad functionality. But it does probably mean that there is some more generic functionality that could be exposed to users, that would allow the users to build the functionality in this PR, plus address all my questions.

Maybe this functionalitiy should be something like

• Search for an amino acid in a nucleotide sequence, given a specific genetic code (with find* functions)
• Allow searches to only search in-frame, somehow.
• Implement findnext, findlast and findall for BioRegex.

This could also be useful to search for other motifs in sequences such as TATA boxes. I'm not sure what this API could look like, but it might be worth thinking about.

I'm closing this PR now, but I'll make an issue to discuss this.