The Computer Language
Benchmarks Game

k-nucleotide Erlang HiPE program

source code

% The Computer Language Benchmarks Game
% http://benchmarksgame.alioth.debian.org/
%% contributed by Fredrik Svahn based on an earlier submission
%%             by Kenneth Johansson, Vlad Dumitrescu and Ulf Wiger

-module(knucleotide).
-export([main/1]).

to_upper(<<C, Cs/binary>>, Acc) when C >= $a, C =< $z ->
    to_upper(Cs, [C-($a-$A)| Acc]);
to_upper(<<$\n, Cs/binary>>, Acc) -> to_upper(Cs, Acc);
to_upper(<<C, Cs/binary>>, Acc) -> to_upper(Cs, [C | Acc]);
to_upper(<<>>, Acc) -> lists:reverse(Acc).

%% Read and discard until start of third segment
seek_three() ->
    case io:get_line('') of
	<<">TH", _/binary>> -> done;
	eof        -> erlang:error(eof);
	_          -> seek_three()
    end.

%% Read third segment
get_seq_three(Seq) ->
    case io:get_line('') of
	eof -> iolist_to_binary(lists:reverse(Seq));
	Str -> get_seq_three([to_upper(Str, [])|Seq])
    end.

%% Generate frequency hash table
gen_freq_table(FreqT, Seq, Len) -> 
    gen_freq_table(Seq, Len, FreqT, size(Seq)-Len).

gen_freq_table(_, _, _, -1) -> done;
gen_freq_table(Seq, Len, FreqT, Dec) ->
    <<_:Dec/binary, Key:Len/binary, _/binary>> = Seq,
    update_counter(Key, FreqT),
    gen_freq_table(Seq, Len, FreqT, Dec-1).

%% Update hash table counter for already existing pattern or insert new
update_counter(Key, FreqT) ->
    try ets:update_counter(FreqT, Key, 1) of _ -> ok
    catch error:badarg -> ets:insert(FreqT, {Key, 1})
    end.

%% Print the frequency table in the right order
print_freq_table(FreqT) ->
    FreqList = lists:reverse(lists:keysort(2, ets:tab2list(FreqT))),
    Tot = lists:foldr(fun({_, Cnt}, Acc)-> Acc + Cnt end, 0, FreqList),
    lists:foreach(fun({Nucleoid, Cnt})->
			  io:fwrite("~s ~.3f\n",[Nucleoid, Cnt*100/Tot]) 
		  end, FreqList),
    io:fwrite("\n").

%% Print number of occurrences for a specific pattern
print_count(FreqT, Pattern) ->
    case ets:lookup(FreqT, Pattern) of
	[{_, Value}] -> io:fwrite("~w\t~s\n",[Value, Pattern]);
	[] -> io:fwrite("~w\t~s\n",[0, Pattern])
    end.

%% Spawn a worker process with its own hash table
do({PrintFun, Pattern}, Seq) ->
    spawn( fun()->
		   FreqT = ets:new(hash, [set]),
		   gen_freq_table(FreqT, Seq, size(Pattern)),
		   %Work is done, wait for token and print
		   receive Pids -> 
			   PrintFun(FreqT, Pattern),
			   hd(Pids) ! tl(Pids) 
		   end,
		   ets:delete(FreqT)
	   end ).

main(_Arg) ->
    io:setopts(standard_io, [binary]),
    seek_three(),
    Seq = get_seq_three([]),
    PrintFreq = fun(Res, _Pattern)-> print_freq_table(Res) end,
    PrintCount = fun(Res, Pattern)-> print_count(Res, Pattern) end,
    Actions = [{PrintFreq,  <<"?">>},
	       {PrintFreq,  <<"??">>},
	       {PrintCount, <<"GGT">>},
	       {PrintCount, <<"GGTA">>},
	       {PrintCount, <<"GGTATT">>},
	       {PrintCount, <<"GGTATTTTAATT">>},
	       {PrintCount, <<"GGTATTTTAATTTATAGT">>}],
	
    Pids = [ do(Action, Seq) || Action <- Actions ],
    %Pass token to print in right order
    hd(Pids) ! tl(Pids) ++ [self()],
    receive _Pid -> halt(0) end.
    

notes, command-line, and program output

NOTES:
64-bit Ubuntu quad core
Erlang/OTP 19 [erts-8.0] [source] [64-bit] [smp:4:4] [async-threads:10] [hipe] [kernel-poll:false]


Thu, 23 Jun 2016 17:23:10 GMT

MAKE:
mv knucleotide.hipe knucleotide.erl
/usr/local/src/otp_src_19.0/bin/erlc +native +"{hipe, [o3]}" knucleotide.erl
rm knucleotide.erl
0.50s to complete and log all make actions

COMMAND LINE:
/usr/local/src/otp_src_19.0/bin/erl -smp enable -noshell -run  knucleotide main 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT