#!/usr/bin/perl -w

use strict;
use autodie;

my ($user_file, $changed_file) = qw{test.txt test.txt.mod};

open my $in_fh, '<', $user_file;
open my $out_fh, '>', $changed_file;

print "Which user? ";
my $user = <STDIN>;
chomp $user;

print $out_fh grep !/^$user,/, <$in_fh>;