kana.sh

#!/bin/bash
# Golfed. 813 chars.
# Original: https://github.com/Qwertylex/bash-kanatrainer
# License: CC BY-SA 3.0.

l="a;i;u;e;o;ka;ki;ku;ke;ko;sa;shi;su;se;so;ta;chi;tsu;te;to;na;ni;nu;ne;no;ha;hi;fu;he;ho;ma;mi;mu;me;mo;ya;yu;yo;ra;ri;ru;re;ro;wa;wo;n"
hira="あいうえおかきくけこさしすせそたちつてとなにぬねのはひふへほまみむめもやゆよらりるれろわをん"
kata="アイウエオカキクケコサシスセソタチツテトナニヌネノハヒフヘホマモムメモヤユヨラリルレロワヲン"
read -ep "hira or kata: " c;a=$(eval echo $`echo ${c}`)
n=0;r=0;t=${#a};IFS=';' read -ra l <<< "$l"
score(){ printf "\n\nScore: %i\nCorrect: %i/%i\n" $((2*$r-$n)) $r $n;exit
};for k in `seq $t | sort -R`;do
let k-=1;trap score SIGINT SIGTERM;i=${l[$k]}
read -ep "${a:$k:1} Romaji?: " w;if [ $i == "$w" ];then
echo Correct!;let r+=1;else
echo Sorry, it was $i.;fi;let n+=1;done
score

On BSD-style Unices, install GNU's coreutils.
On OS X with Homebrew, you'll now have gsort so you'll have to modify the script (line 12).