I have a file that looks like this:
I am using the following script to report if AATTCCGGATCG is present in any sequence:
However, what I really need is the four characters right after the given string (AATTCCGG), in my example=ATCG. Importantly, the string can be found reversed GGCCTTAA and complemented A=T; T=A; C=G and G=C, originating the following string =CCGGAATT in the sequence. If the string is found reversed and complemented, the four characters after the string must be reported as reversed and complemented. Thus, the desired output from a file containing the following sequences:
would be AACG, since sequence 2 contains the corresponding string, only reversed and complemented.
My script can deal with the fact that the sequence is reversed/complemented. However, if any of the positions after the string is mutated, it will not detect it. That's is why I would rather get the characters instead
Any help will be greatly appreciated
Thanks
PS. The string, in this case AATTCCGG or CCGGAATT will never be mutated in a real scenario.
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