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Editorial Team
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Asked: 2026-05-16T00:08:18+00:00

I’m trying to get the mean length of fasta sequences using Erlang . A

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I’m trying to get the mean length of fasta sequences using Erlang. A fasta file looks like this

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

I tried to answser this question using the following Erlang code:

-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().

Compilation/Execution:

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

this code seems to work fine for a small fasta file but it takes hours to parse a larger one (>100Mo). Why ? I’m an Erlang newbie, can you please improve this code ?

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1 Answer

  1. Editorial Team

    If you need really fast IO then you have to do little bit more trickery than usual.

    -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.

    It is fastest IO as I know but note -noshell -noinput.
    Compile just like erlc +native +"{hipe, [o3]}" g.erl but with -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

    and run:

    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

    With -smp enable but native it takes:

    $ 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

    Byte code but with -smp disable (almost in par with native because most of work is done in port!):

    $ 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

    Just for completeness byte code with 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

    For comparison sarnold version gives me wrong answer and takes more on same HW:

    $ 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

    EDIT: I have looked at characteristics of uniprot_sprot.fasta and I’m little bit surprised. It is 3824397 rows and 232MB. It means that -smp disabled version can handle 1.18 million text lines per second (71MB/s in line oriented IO).

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