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if($min == 0)
{
...
    $scoring = 0.2;
}
print $fh "$fields[0], $field2, $valid_protein, $field3, $min, $scorin
+g\n";

my $valid_protein = 'no valid protein';

...
}

print $fh "$fields[0], $field2, $valid_protein, $field3, $min, $scorin
+g\n";