adding new alignment package and global alignment via Needleman-Wunsch #288
Conversation
…ent traceback next.
|
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. |
|
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 |
#288) * initial implementation of global alignment via NeedlemanWunsch * test coverage 100% * added wikipedia link for Needleman-Wunsch * added corner case tests at the suggestion of Daniel Liu @daniel_c0deb0t via twitter
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