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$dbh->do(<<SQL);
-- create first temp table
...
$dbh->do(<<SQL);
-- create third temp table
SQL

for my $file ("first.sql", "second.sql", "third.sql") {
    open my $fh, '<', $file or die "$file: $!";
...
    my $sql = <$fh>;
    $dbh->do( $sql );
}