I'm not sure you've given enough information. We need a broader selection of example inputs and outputs.

For instance, here's a perfectly valid script that does exactly what you demand -- no more, no less:

#!/usr/bin/perl
#       xyzatgc.pl
#       =  Copyright 2011 Xiong Changnian <xiong@cpan.org>   =
#       = Free Software = Artistic License 2.0 = NO WARRANTY =

use 5.014002;
use strict;
use warnings;

#~ use Devel::Comments '#####', ({ -file => 'debug.log' });

#---------------------------------------------------------------------
+-------#

# Pass input filename on command line: $ xyzatgc.pl infile.txt
my $in_filename     = shift;

# Construct output filename: infile.txt => infile.out
$in_filename       =~ /([^.]+)\.txt/;
my $out_filename    = $1 . q|.out|;

# Slurp in entire input file.
my $indata          ;
{
    open my $in_fh, '<', $in_filename
        or die "Couldn't open $in_filename for reading";
    local $/        = undef;            # slurp
    $indata         = <$in_fh>;
    close $in_fh 
        or die "Couldn't close $in_filename";
};

# Substitute as required.
$indata     =~ s/XYZATGC/XYZ/g;

# 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";

# Terminate.
say 'Done.';

__END__
[download]

Input:

XYZATGC XYZATGC XYZATGC XYZATGC XYZATGC 
XYZ xyz foo ATGC atgc JAPHATGC
XYZATGC 
XYZATGCXYZATGCXYZATGC
[download]

Output:

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

Now I'm going to wager that's not quite what you want. Please don't try to explain in English words what you'd rather see. Instead, show us a fuller example of input and output.

We'll see what we can do.