Hello choroba,

Yes I have tried and the code you have given works perfectly with the example above. Thanks very much :) I very much appreciate.

But the problem I am facing is In my File2, I have many more cases. For Example: string1 in File1 has two positions highlighted (1st and 3rd). However in File2, we may have more positions mentioned. For instance, we have "string1 20 A T" (3rd line), which is out of range and has to be omitted.

File1:

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

[download]

File2:

string1 1 C A 
string1 3 T C 
string1 20 A T  /* This is out of range, and has to be omitted*/
string2 2 A C 
string2 5 A T 
string2 9 G A 
string2 30 A C /* This is out of range, and has to be omitted*/
string3 9 G A /* This string is not there in the main file.. so has to
+ be omitted */

[download]

And in such case of File2, it`s not working. And I have a File2 of a billion lines.

In reply to Re^4: Looking for Printing all possible combinations by sarkar
in thread Looking for Printing all possible combinations by sarkar

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