Yes you are correct, my mistake

By the way, thanks for the code!

It works great, here is the complete version that reads from and writes to files.

use strict; 
use warnings; 

print "\n Running script for Jiggs \n";
my $infile = "foot.txt";                   

open my $in,  "<", $infile     or die $!;  
open my $out, ">", "foot1.txt" or die $!;

my $line;     
while ( <$in> ) {
    chomp;
    s/length=//;
    s/xy=//g;
    s/region=//g;
    s/run=//g;
    tr/ /,/s;
    if ( /^>/ ) {
        print $out "$line\n" if $line;
        $line = $_;
        }
    else {
        $line .= $_;
        }
    }           
print $out "$line\n";


close $in; 
close $out; 
 
print "\n Done!\n";
[download]

Many thanks to all the responses, I learned so much today: Using RegEx's and substitution, file handling, split function, and joining arrays!