"fasta文件中序列的平均长度":你能改进这个Erlang代码吗？

Question

我正在尝试使用Erlang获取fasta序列的平均长度.fasta文件看起来像这样

>title1
ATGACTAGCTAGCAGCGATCGACCGTCGTACGC
ATCGATCGCATCGATGCTACGATCGATCATATA
ATGACTAGCTAGCAGCGATCGACCGTCGTACGC
ATCGATCGCATCGATGCTACGATCTCGTACGC
>title2
ATCGATCGCATCGATGCTACGATCTCGTACGC
ATGACTAGCTAGCAGCGATCGACCGTCGTACGC
ATCGATCGCATCGATGCTACGATCGATCATATA
ATGACTAGCTAGCAGCGATCGACCGTCGTACGC
>title3
ATCGATCGCATCGAT(...)

我尝试使用以下Erlang代码回答这个问题:

-module(golf).
-export([test/0]).

line([],{Sequences,Total}) ->  {Sequences,Total};
line(">" ++ Rest,{Sequences,Total}) -> {Sequences+1,Total};
line(L,{Sequences,Total}) -> {Sequences,Total+string:len(string:strip(L))}.

scanLines(S,Sequences,Total)->
        case io:get_line(S,'') of
            eof -> {Sequences,Total};
            {error,_} ->{Sequences,Total};
            Line -> {S2,T2}=line(Line,{Sequences,Total}), scanLines(S,S2,T2)
        end  .

test()->
    {Sequences,Total}=scanLines(standard_io,0,0),
    io:format("~p\n",[Total/(1.0*Sequences)]),
    halt().

编译/执行:

erlc golf.erl
erl -noshell -s golf test < sequence.fasta
563.16

这个代码似乎适用于一个小的fasta文件,但解析一个较大的(> 100Mo)需要几个小时.为什么？我是Erlang的新手,请你改进这段代码吗？

Answer 1

如果你需要非常快的IO,那么你必须比平常做更多的技巧.

-module(g).
-export([s/0]).
s()->
  P = open_port({fd, 0, 1}, [in, binary, {line, 256}]),
  r(P, 0, 0),
  halt().
r(P, C, L) ->
  receive
    {P, {data, {eol, <<$>:8, _/binary>>}}} ->
      r(P, C+1, L);
    {P, {data, {eol, Line}}} ->
      r(P, C, L + size(Line));
    {'EXIT', P, normal} ->
      io:format("~p~n",[L/C])
  end.

据我所知,这是最快的IO -noshell -noinput.编译就像erlc +native +"{hipe, [o3]}" g.erl但是-smp disable

erl -smp disable -noinput -mode minimal -boot start_clean -s erl_compile compile_cmdline @cwd /home/hynek/Download @option native @option '{hipe, [o3]}' @files g.erl

并运行:

time erl -smp disable -noshell -mode minimal -boot start_clean -noinput -s g s < uniprot_sprot.fasta
352.6697028442464

real    0m3.241s
user    0m3.060s
sys     0m0.124s

有-smp enable本地需要:

$ erlc +native +"{hipe, [o3]}" g.erl
$ time erl -noshell -mode minimal -boot start_clean -noinput -s g s<uniprot_sprot.fasta
352.6697028442464

real    0m5.103s
user    0m4.944s
sys     0m0.112s

字节代码,但-smp disable(几乎与本机相同,因为大多数工作是在端口完成的!):

$ erlc g.erl
$ time erl -smp disable -noshell -mode minimal -boot start_clean -noinput -s g s<uniprot_sprot.fasta
352.6697028442464

real    0m3.565s
user    0m3.436s
sys     0m0.104s

只是为了完整性字节代码与smp:

$ time erl -noshell -mode minimal -boot start_clean -noinput -s g s<uniprot_sprot.fasta 
352.6697028442464

real    0m5.433s
user    0m5.236s
sys     0m0.128s

为了比较sarnold 版本给了我错误的答案,并在同一硬件上采取更多:

$ erl -smp disable -noinput -mode minimal -boot start_clean -s erl_compile compile_cmdline @cwd /home/hynek/Download @option native @option '{hipe, [o3]}' @files golf.erl
./golf.erl:5: Warning: variable 'Rest' is unused
$ time erl -smp disable -noshell -mode minimal -s golf test
359.04679841439776

real    0m17.569s
user    0m16.749s
sys     0m0.664s

编辑:我看过的特点,uniprot_sprot.fasta我有点惊讶.它是3824397行和232MB.这意味着该-smp disabled版本每秒可处理118万个文本行(面向行的IO为71MB/s).