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#!/usr/bin/perl -w
use strict;
...
    $EXON_IN = <test.txt>;
    print "$i, -$EXON_IN-\n";
}

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