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open (INPUTFILE, "< $filein");
while (<INPUTFILE>) {
    my $line=$_;
    $line =~ s/\),\(/\)\n\(/gi;
};

my $regex=<STDIN>;                    #Entering s/\),\(/\)\n\(/gi 
chomp $regex;
...
    my $line=$_;
    $line =~ $regex;
};