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s312569 / clj-biosequence

A Clojure library designed to make the manipulation of biological sequence data easier.
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Auto-capitalize checked alphabets #33

Closed averagehat closed 8 years ago

averagehat commented 8 years ago

closes #32
also tests string storage also travis-ci closes #34

s312569 commented 8 years ago

Brilliant thanks! The only comment I would have is that lower case letters are often used for soft masking sequences so it is probably desirable that the sequence strings retain their case.

I've set up a branch (averagehat-master) based on your fork where the characters are upper-cased before checking but if they pass the original case is used in the string. I also amended the codon->aa and revcom functions in the alphabet file to upper-case characters before doing their thing. Also added a test for translation using lower-case letters. If you are happy with that I can merge into master.

Also added the repository to www.travis-ci.com.

Thanks!