use strict; 
use warnings; 

print "\n Running script for Jiggs \n";
my $infile = "foot.txt";                   # <foot.txt> is not legal quotation in perl5

open my $in,  "<", $infile     or die $!;  # Don't quote a variable again
open my $out, ">", "foot1.txt" or die $!;

my $line = <$in>;                          # Is $line the header? If so, don't call it "line"
$line =~ s/\s+\Z/\n/;                      # When you chomp, you don't get a "new" newline
$line =~ s/ +/,/g;
print $out $line;                          # Don't quote variable. It now still has a newline
print $out scalar <$in>;                   # What is this second line? Something special?

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

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