UNIX for Dummies Questions & Answers

Hi Unix Gurus,

I have a file with data like:

Code:

>header_1
TCCCCGA
>header_2
CCAATTGGGTA

The data to work with starts from the next line after '>header_xx'.
(1)
I want to search the three letter patterns 'CHH' or 'DDG' and replace C and G by exclamation ! so that CHH becomes !HH and DDG becomes DD!.
where: H = any letter but not G (example CHH = CAA, CAT, CTT etc) and D = any letter but not C (example DGG = ATG, AAG etc)
(2)Form a 3 letter window and slide 1 letter at a time; check for the patten described above until finish replacing.
Example output:

Code:

>header_1
T!!CCGA
>header_2
!!AATT!!!TA

Thanks a lot for your help.

Try this (yields the desired result without formally forming a 3 letter window):

Code:

awk     '       {while (gsub(/C[^G][^G]/, "@&")) gsub(/@C/,"!")}
                {while (gsub(/[^C][^C]G/, "&@")) gsub(/G@/,"!")}
         1
        ' file
>header_1
T!!CCGA
>header_2
!!AATT!!!TA

To be honest, i have troubles understanding the exact meaning of this. I suppose you want to work on different reading frames.

Because there are only 3 of them (using "T" as any triplett and "B" for any single base there is only "TTT...", "BTTT..." and "BBTTT...") you will not need a sliding window.

Second, because of your first replacements a pattern could match where it hasn't matched before in subsequent passes. Suppose your line is:

Code:

DDGG

Because it will not match "DDG" the triplett 2-4 would not be replaced. Once triplett 1-3 would be replaced, it would match, though:

Code:

DDGG        # replace "DDG" with "DD!"
DD!G        # after first replacement, now prelace "2 not-Gs, then G" again
DD!!        # after second pass

Analogous for your other replacement rules. Somehow i doubt that this is what you really want. Please clarify.

I hope this helps.

bakunin

Hi bakunin
thanks for taking the time to go through it and providing the example.
you are right:
DD!! # after second passis exactly what I need.
This is irrespective of the codon, reading frame etc and to do with replacing the C's in the CHH methylation context.
So it'll be really helpful if a piece of code that will be able to it in multiple pass as you explained.