This looks fine to my eyes; the only objection is the annoying amount of markup required:

# Write results to output file.
open my $out_fh, '>', $out_filename
    or die "Couldn't open $out_filename for writing";
say {$out_fh} $indata;
close $out_fh 
    or die "Couldn't close $out_filename";
[download]

XYZ XYZ XYZ XYZ XYZ 
XYZ xyz foo ATGC atgc JAPHATGC
XYZ 
XYZXYZXYZ
[download]

Note that my Display Settings are as shown in Line Numbering in Code Listings.