#!/usr/bin/perl
use warnings;
use strict;

sub alternate {
    my ($id, $string, @changes) = @_;
    unless (@changes) {
        print "$id $string\n";
        return
    }

    # The variant with the original character.
    my ($bracket, $char) = @{ shift @changes };
    alternate($id, $string, @changes);

    # The variant with the alternative character.
    $string =~ /\(/g for 1 .. $bracket;    # Find the bracket.
    substr $string, pos $string, 1, $char;
    alternate($id, $string, @changes);
}


open my $STRINGS, '<', 'File1' or die $!;
open my $ALTS,    '<', 'File2' or die $!;

while (my $string_line = <$STRINGS>) {
    my ($string_id, $string) = split ' ', $string_line;
    # Count the bracketed parts.
    my $count = ((my $bare_string = $string) =~ s/[()]//g) / 2;

    my @changes;

    for my $bracket (1 .. $count) {
        my $alt_line = <$ALTS>;
        my ($alt_id, $pos, $orig, $alt) = split ' ', $alt_line;

        die "Out of sync: $string_id != $alt_id\n" if $string_id ne $a
+lt_id;

        my $char = substr $bare_string, $pos - 1, 1;
        die "Invalid char at pos $pos in $string_id: $orig != $char\n"
            if $orig ne $char;

        push @changes, [ $bracket, $alt ];
    }
    alternate($string_id, $string, @changes);
}
[download]

It might be a bit too complex for a newbie, but the task is not really simple, either.

Hello choroba, Thank you very much. I highly appreciate. I am trying to understand the code. But I have one question. I have multiple positions with Brackets (for example I have given 3). What do I need to modify so that it works for multiple brackets in File1 and many such strings in file2. I have around 1million entries in File2. Many Thanks.

The code given here generates exactly the output you requested. Do you understand recursion?
لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

Like for Example In File 1: I have given string2 T(A)GG(A)GGG(G) But it can have multiple brackets in different strings such as TAA(A)G(T)G(A)GGAG(G)CCA(A) How does it work? What should I modify in the code? And also my File2 is really big with a million Entries.

I am very new to PERL would highly appreciate if somebody can help me with this.

Sure, here you go, perlintro, open, readline, combinations, combinations, combinations

Nothing wrong per se in cross-posting questions on several sites, but it is considered polite to inform people of that and provide links, to avoid duplication of work at various parts of the Internet.

Hello Laurent R, Thank you for letting me know. I was unaware of it and ones I have a workout out completely, I thought of posting it to the other forums so that if someone is looking for similar things they can benefit from it.

Yes, by all means, publish there the solutions you got here, and vice_versa, that's great.

But it is still better to let people know upfront, because even if you don't have a complete solution here, or don't know if it is complete, so that you don't yet inform others yet about the progress here, I might be working on the other site on an even less complete solution. When I first saw your post (on the PG forum), I was in the train commuting from work to home, and I read your post on a mobile device. I was not going to try to provide a solution to this relatively complex problem in these conditions. But if I had been sitting in front of a computer, I might have tried, not knowing that Choroba had possibly already offered here a solution that is perhaps better than what I would have tried to provide.

Je suis Charlie.

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]

Hello Anonymous Monk,

Thank you very much. I completely agree with you. Not at all newbie friendly. But I have one more question.

Like for Example In File 1: I have given the string2 T(A)GG(A)GGG(G). But my original file has multiple brackets in different strings such as TAA(A)G(T)G(A)GGAG(G)CCA(A). An example provided below. What should I modify in the code? And also my File2 is really big with a million Entries.

If my file1:

string1 (C)C(T)A
string2 T(A)GG(A)GGG(G)
string3 T(A)GG(A)GGG(G)AAAAAAA(C)ACT(G)
string4 TAA(A)G(T)G(A)GGAG(G)CCA(A)
[download]

What would you suggest?

Both this solution and my solution support any number of brackets. Why haven't you tried it?
لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ