#!/usr/bin/perl -w
use strict;

my $EXON_IN;
for (my $i=0; $i < 5; $i++){
    $EXON_IN = <test.txt>;
    print "$i, -$EXON_IN-\n";
}

##</code><code>##

[scott@blast test]$ ./test.pl
0, -test.txt-
Use of uninitialized value in concatenation (.) or string at ./test.pl line 7.
1, --
2, -test.txt-
Use of uninitialized value in concatenation (.) or string at ./test.pl line 7.
3, --
4, -test.txt-