Fastest Way To Find Mismatch Positions Between Two Strings of the Same Length

Question

I have a millions of pairs of string of same length which I want to compare and find the position where it has mismatches.

For example for each $str1 a

Answer 1

Here is a benchmarking script to figure out if the differences in speed of various approaches. Just keep in mind that there will be a lag the first time a script using Inline::C is invoked as the C compiler is invoked etc. So, run the script once, and then benchmark.

#!/usr/bin/perl

use strict;
use warnings;

use Benchmark qw( cmpthese );

my ($copies) = @ARGV;
$copies ||= 1;

my $x = 'ATTCCGGG' x $copies;
my $y = 'ATTGCGGG' x $copies;
my $z = 'ATACCGGC' x $copies;

sub wrapper { 
    my ($func, @args) = @_;
    for my $s (@args) {
        my $differences = $func->($x, $s);
        # just trying to ensure results are not discarded
        if ( @$differences == 0 ) { 
            print "There is no difference\n";
        }
    }
    return;
}

cmpthese -5, {
    explode  => sub { wrapper(\&where_do_they_differ, $y, $z) },
    mism_pos => sub { wrapper(\&mism_pos, $y, $z) },
    inline_c => sub {
        wrapper(\&i_dont_know_how_to_do_stuff_with_inline_c, $y, $z) },
};

sub where_do_they_differ {
    my ($str1, $str2) = @_;
    my @str1 = split //, $str1;
    my @str2 = split //, $str2;
    [ map {$str1[$_] eq $str2[$_] ? () : $_} 0 .. length($str1) - 1 ];
}

sub mism_pos {
    my ($str1, $str2) = @_;
    my @mism_pos;

    for my $i (0 .. length($str1) - 1) {
        if (substr($str1, $i, 1) ne substr($str2, $i, 1) ) {
            push @mism_pos, $i;
        }
    }
    return \@mism_pos;
}

sub i_dont_know_how_to_do_stuff_with_inline_c {
    [ find_diffs(@_) ];
}

use Inline C => << 'EOC';
    void find_diffs(char* x, char* y) {
        int i;
        Inline_Stack_Vars;
        Inline_Stack_Reset;
        for(i=0; x[i] && y[i]; ++i) {
            if(x[i] != y[i]) {
                Inline_Stack_Push(sv_2mortal(newSViv(i)));
            }
        }
        Inline_Stack_Done;
    }
EOC

Results (using VC++ 9 on Windows XP with AS Perl 5.10.1) with $copies = 1:

            Rate  explode mism_pos inline_c
explode  15475/s       --     -64%     -84%
mism_pos 43196/s     179%       --     -56%
inline_c 98378/s     536%     128%       --

Results with $copies = 100:

            Rate  explode mism_pos inline_c
explode    160/s       --     -86%     -99%
mism_pos  1106/s     593%       --     -90%
inline_c 10808/s    6667%     877%       --