There does not seem to be anything wrong with the code you posted. I understand it can be difficult to write an SSCCE when you do not know what is wrong. Perhaps this will help. As you can see, the following code does what I think you want without error. Please modify it to demonstrate your error. Post the failing code. Remember, we have to be able to run it and reproduce your error message. 
>type crickson.pl
use strict;
use warnings;
my $arg = \'$infile1';
my $infile1 = \"one_score\t999";

my $score=100000;
open my $IN, '<', $arg or die "error opening list of files";
while (<$IN>) {
    $_ = eval $_;   # Bad practice - Use only for 'in-memory' file.
    open my $IN1, '<', $_ or die "error opening file $_";
    while (local $_ = <$IN1>) {
        my @temp = split /\t/;
        if ($temp[1] < $score) {
            warn "\$temp[1] not defined\n" if !defined $temp[1];
            warn "\$score not defined\n" if !defined $score;
            print  "$temp[1] < $score\n";
        }
    }
}

>perl crickson.pl
999 < 100000

>

[download]
Bill

In reply to Re: Variable scope issue by BillKSmith
in thread Variable scope issue by crickson

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