if($min == 0)
{
    $scoring = 1;
    my $valid_protein = $each_protein;

}
elsif($min == 1)
{
    $scoring = 0.5;
}
else
{
    $scoring = 0.2;
}
print $fh "$fields[0], $field2, $valid_protein, $field3, $min, $scorin
+g\n";
[download]

If 'the field "valid_protein"' is related to the  $valid_protein lexical scalar, be aware that this scalar does not exist outside of the first if-block quoted above. The scalar  $valid_protein in the statement
    print $fh "$fields[0], $field2, $valid_protein, $field3, $min, $scoring\n";
has never been defined and has no value. warnings would have told you about this; strict would have prevented it.

Update: A simple fix would be to define the lexical outside the if-block, then later use it. Note, however, that this scalar is only assigned a value within the if-block, so it would be wise to initialize the scalar with some default value when it is defined:

my $valid_protein = 'no valid protein';

if($min == 0)
{
    $scoring = 1;
    $valid_protein = $each_protein;
}
elsif($min == 1)
{
    $scoring = 0.5;
}
else
{
    $scoring = 0.2;
}

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

And BTW:  $scoring is never defined as a lexical anywhere; is this what you really want? (Maybe take a look at the free Modern Perl download.)