What isn't working about it? It works for me; I added some code to dump out aliases (using Data::Dumper) and it contains the correct data:

    % test.pl
    ca foo->bar

    $VAR1 = {
          'foo' => 'bar'
        };
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An alternate way of doing this, rather than using split, would be to use matching parens in the regular expression that you already have:

    if ($in =~ /^(\w{2})\s+(\w+)->(\w+)$/) {
        my($command, $key, $value) = ($1, $2, $3);
        $aliases{$key} = $value;
    }
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This would work if your commands are always 2 characters long, and if they always have the same format with the "->".