Sorry this isn't newbie friendly:

open my $f1, '<', \<<'';
string1 (C)C(T)A
string2 T(A)GG(A)GGG(G)

open my $f2, '<', \<<'';
string1 1 C A
string1 3 T C
string2 5 A T
string2 9 G A
string2 2 A C

my %h = map split, <$f1>;
tr/()//d, $_ = [split //] for values %h;

while (<$f2>) {
    local $" = ',';
    my ($k, $i, @combo) = split;
    $h{$k}[$i-1] = lc "{@combo}";
}

for my $k (sort keys %h) {
    local $" = '';
    while (<@{$h{$k}}>) {
        s/([a-z])/(\u$1)/g;
        print "$k $_\n";
    }
}

[download]

Outputs:

string1 (C)C(T)A
string1 (C)C(C)A
string1 (A)C(T)A
string1 (A)C(C)A
string2 T(A)GG(A)GGG(G)
string2 T(A)GG(A)GGG(A)
string2 T(A)GG(T)GGG(G)
string2 T(A)GG(T)GGG(A)
string2 T(C)GG(A)GGG(G)
string2 T(C)GG(A)GGG(A)
string2 T(C)GG(T)GGG(G)
string2 T(C)GG(T)GGG(A)

[download]

In reply to Re: Looking for Printing all possible combinations by Anonymous Monk
in thread Looking for Printing all possible combinations by sarkar

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