How did you do it? Unless you post code we can't tell what went wrong. Works fine for me

my @one = split /,/, '1,2,3,4,5,6';
my @two = split /,/, '2,9,8,4,7,6';
my @result;
for my $i ( 0 .. $#one ) {
    push @result, $one[$i] - $two[$i];
}
my $result = join ',', @result;
print $result, "\n";

__END__
-1,-7,-5,0,-2,0
[download]

Update: As suggested by j1n3l0

use List::MoreUtils qw(pairwise);

my @one = split /,/, '1,2,3,4,5,6';
my @two = split /,/, '2,9,8,4,7,6';

our ($a, $b);  # keep warnings happy
my $result = join ',', pairwise { $a - $b } @one, @two;
[download]

Thanks, just reread the doco for List::MoreUtils. I really must remember to do that anytime there is a list processing problem that doesn't quite fit standard techniques

use strict;
use warnings;
use PDL;

my $first  = pdl qw/1 2 3 4 5 6/;
my $second = pdl qw/2 9 8 4 7 6/;

my $result = $first - $second;

print "$result\n";
[download]

Some code would have been nice, but you can try push( @c, shift(@a) - shift(@b)) while (@a and @b); It is destructive, but @c will contain the results when it is done and it.

or a non-descructive version  $c[$_] =  $a[$_] - $b[$_] for  0 ..  ($#a <  $#b ? $#a : $#b);, but I think the first is easier to read. ;)

Updated thanks to some comments from ysth regarding precedence and a typo )

#!/usr/bin/perl

use strict;
use warnings;

### open(FILEIN, "table.txt"); #numbers table which only has 0 and 1.
### let's read from __DATA__ instead (try adding your own DATA...)

open FILEOUT, ">>data.txt" or die "data.txt: $!\n";
### opens data.txt in output/append mode

my @seed = split //, "01110011001111100010111101011111000100110";
my $expected = scalar @seed;

while (<DATA>) {  ### reads line by line from DATA which is provided b
+elow
    chomp;        ### you do want to chomp the input
    if ( ! /^[01]+$/ ) {
        warn "input line $. has characters other than 0 and 1\n";
        next;
    }
    my $length = length();
    if ( $length != @seed ) {
        warn "input line $. has $length digits instead of $expected\n"
+;
    }
    my $count = 0;
    for my $digit ( split // ) {
        $seed[$count++] -= $digit;
    }

    print FILEOUT "@seed\n";  #shows you what we have read
}
### close FILEIN;
close FILEOUT;

__DATA__
01110011001111100010111101011111000100110
01110011001111100010111101011111000100110
1110011001111100010111101011111000100110
0011100110011111000101111010111110001001101
012345
xyz
[download]

• uses a shorter sample string for creating @seed (just for the sake of easier posting)

• actually puts something into @seed -- your version does not: you assign a string to "$input", but this variable is not used anywhere else

• includes sample data with the script, so that it can be run without having to open an external input file (which you did not provide); the sample data consists of a copy of the "seed" string, along with a few simple variations to test things out.

• includes some sanity checks on the input: (a) reject a line that contains anything other than 0's and 1's (but your initial example used other digits, so maybe you don't want this?), and (b) issue warnings for lines with unexpected lengths (but go ahead and use them)

• avoids the use of unnecessary variables and the  @seed[$count] mistake, and includes "use strict" and "use warnings" (which pointed out that mistake)

When I ran it, everything in the output was integers (no fractional numbers with decimal points). Of course. since values are being subtracted from the seed array, (which started with 0's and 1's), the results end up as negative decimal values (e.g. if seed starts with "0" in a given position, and the first two lines of input have "1" in that position, you get "-2").

If you were hoping to get binary digit results, what do you expect "0 - 1 - 1" to produce? Maybe you want some sort of bitwise operation instead of integer subtraction? Check out perlop (look for "bitwise"), as well as the vec, pack and unpack functions. Hint: try this:

#!/usr/bin/perl -l

$a="0101"; $b="1110";
print "$a & $b = " . ($a & $b);
print "$a | $b = " . ($a | $b);
print "$a ^ $b = " .(($a ^ $b) | "0000"); # this one is a little trick
+y

__OUTPUT__
0101 & 1110 = 0100
0101 | 1110 = 1111
0101 ^ 1110 = 1011
[download]

Can you demonstrate the problem you mentioned (getting "float" numbers) using some sample data of your own? If so, please show us that data.