Fast Way to Find Difference between Two Strings of Equal Length in Perl

Question

Given pairs of string like this.

    my $s1 = \"ACTGGA\";
    my $s2 = \"AGTG-A\";

   # Note the string can be longer than this.

I would

Answer 1

I was bored on Thanksgiving break 2012 and answered the question and more. It will work on strings of equal length. It will work if they are not. I added a help, opt handling just for fun. I thought someone might find it useful. If you are new to PERL add don't know. Don't add any code in your script below DATA to the program. Have 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 = ;
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__