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bebop / poly

A Go package for engineering organisms.
https://pkg.go.dev/github.com/bebop/poly
MIT License
665 stars 70 forks source link

adding new alignment package and global alignment via Needleman-Wunsch #288

Closed TimothyStiles closed 1 year ago

TimothyStiles commented 1 year ago

Poly needs a basic alignment algo to compare sequences. Needleman-Wunsch is about as basic as it gets as far as I know and its implementation is only 70 lines or so.

I'm a little unsure of what sort of corner cases I should use to test it and I'm interested to hear if there's a better way to structure calls and pass parameters to align.NeedlemanWunsch. Otherwise everything is clean and code coverage is 100%.

-Tim

TimothyStiles commented 1 year ago

Just added the local alignment algorithm SmithWaterman as well but have yet to implement a traceback to return and it just returns the distance metric score by itself.

TimothyStiles commented 1 year ago

I'm not completely satisfied but this is good enough to ship. Documentation is okay but needs more. I'd like a whole section on alignment algos but they aren't exactly my forte so any guest documentation would be greatly appreciated.

I've moved some SmithWaterman related stuff to two other branches. I somewhat blackboxed getting my implementation to produce the score correctly but am I little lost on how to get the traceback to produce alignments.

Including things like blosum matrices would be a nice update but I don't personally need it now. Would be happy to include if someone makes a PR!

-Tim