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 $!;

while (<$in>) {
    
    s/\s+\Z/\n/;
    s/ +/,/g;
    s/,length=/,/g;
    s/,xy=/,/g;
    s/,region=/,/g;
    s/,run=/,/g;
    
    print $out $_;
    }

close $in; 
close $out; 
 
print "\n Done!\n";