A quick way to find the difference between two lines of equal length in Perl

Question

Data pairs of such lines.

my $s1 = "ACTGGA"; my $s2 = "AGTG-A"; # Note the string can be longer than this. 

I would like to find position and character in $s1 , where it differs from $s2 . In this case, the answer will be as follows:

 #String Position 0-based # First col = Base in S1 # Second col = Base in S2 # Third col = Position in S1 where they differ CG 1 G - 4 

I can easily achieve this with substr() . But it is terribly slow. Usually I need to compare millions of such pairs.

Is there a quick way to achieve this?

Answer 1

Stringwise ^ is your friend:

 use strict; use warnings; my $s1 = "ACTGGA"; my $s2 = "AGTG-A"; my $mask = $s1 ^ $s2; while ($mask =~ /[^\0]/g) { print substr($s1,$-[0],1), ' ', substr($s2,$-[0],1), ' ', $-[0], "\n"; } 

EXPLANATION:

The ^ operator (exclusive or) used in strings returns a string consisting of the result of the exception or each bit of the numeric value of each character. Breakdown of the example into equivalent code:

 "AB" ^ "ab" ( "A" ^ "a" ) . ( "B" ^ "b" ) chr( ord("A") ^ ord("a") ) . chr( ord("B") ^ ord("b") ) chr( 65 ^ 97 ) . chr( 66 ^ 98 ) chr(32) . chr(32) " " . " " " " 

A useful feature here is that a nul character ( "\0" ) occurs if and only if two lines have the same character at that position. Therefore, ^ can be used to effectively compare each character of two lines in one quick operation, and as a result, non-zero characters can be searched (indicating the difference). The search can be repeated using the / g regex flag in a scalar context, and the position of each character difference is found using $-[0] , which gives the start offset of the last successful match.

Answer 2

Use the ops binary bits for all strings.

Things like $s1 & $s2 or $s1 ^ $s2 work incredibly fast and work with strings of arbitrary length.

Answer 3

I was bored in Thanksgiving in 2012 and answered a question and more. It will work on strings of equal length. It will work if it is not. I added help, I prefer to just have fun. I thought someone might find this helpful. If you are new to PERL add, you don’t know. Do not add the code << → DATA to the script program. Have some fun.

./diftxt -h

  usage: diftxt [-v ] string1 string2 -v = Verbose diftxt [-V|--version] diftxt [-h|--help] "This help!" Examples: diftxt test text diftxt "This is a test" "this is real" Place Holders: space = "·" , no charater = "ζ" 

cat./diftxt ----------- cut ✂ ----------

 #!/usr/bin/perl -w use strict; use warnings; use Getopt::Std; my %options=(); getopts("Vhv", \%options); my $helptxt=' usage: diftxt [-v ] string1 string2 -v = Verbose diftxt [-V|--version] diftxt [-h|--help] "This help!" Examples: diftxt test text diftxt "This is a test" "this is real" Place Holders: space = "·" , no charater = "ζ"'; my $Version = "inital-release 1.0 - Quincey Craig 11/21/2012"; print "$helptxt\n\n" if defined $options{h}; print "$Version\n" if defined $options{V}; if (@ARGV == 0 ) { if (not defined $options{h}) {usage()}; exit; } my $s1 = "$ARGV[0]"; my $s2 = "$ARGV[1]"; my $mask = $s1 ^ $s2; # setup unicode output to STDOUT binmode DATA, ":utf8"; my $ustring = <DATA>; binmode STDOUT, ":utf8"; my $_DIFF = ''; my $_CHAR1 = ''; my $_CHAR2 = ''; sub usage { print "\n"; print "usage: diftxt [-v ] string1 string2\n"; print " -v = Verbose \n"; print " diftxt [-V|--version]\n"; print " diftxt [-h|--help]\n\n"; exit; } sub main { print "\nOrig\tDiff\tPos\n----\t----\t----\n" if defined $options{v}; while ($mask =~ /[^\0]/g) { ### redirect stderr to allow for test of empty variable with error message from substr open STDERR, '>/dev/null'; if (substr($s2,$-[0],1) eq "") {$_CHAR2 = "\x{03B6}";close STDERR;} else {$_CHAR2 = substr($s2,$-[0],1)}; if (substr($s2,$-[0],1) eq " ") {$_CHAR2 = "\x{00B7}"}; $_CHAR1 = substr($s1,$-[0],1); if ($_CHAR1 eq "") {$_CHAR1 = "\x{03B6}"} else {$_CHAR1 = substr($s1,$-[0],1)}; if ($_CHAR1 eq " ") {$_CHAR1 = "\x{00B7}"}; ### Print verbose Data print $_CHAR1, "\t", $_CHAR2, "\t", $+[0], "\n" if defined $options{v}; ### Build difference list $_DIFF = "$_DIFF$_CHAR2"; ### Build mask substr($s1,"$-[0]",1) = "\x{00B7}"; } ### end loop print "\n" if defined $options{v}; print "$_DIFF, "; print "Mask: \"$s1\"\n"; } ### end main if ($#ARGV == 1) {main()}; __DATA__ 

Answer 4

This is the easiest form you can get.

 my $s1 = "ACTGGA"; my $s2 = "AGTG-A"; my @s1 = split //,$s1; my @s2 = split //,$s2; my $i = 0; foreach (@s1) { if ($_ ne $s2[$i]) { print "$_, $s2[$i] $i\n"; } $i++; }