Being a bit short on time i will deal only with the first part:

No, your solution is good. It is possible to do the same in awk, though, and if you want to use awk anyway for the second part of your requirement you might want to do all in one pass instead of doing something like sed '....' file | awk '....'. This, of course, is only the case if your two requirements are always two parts of one step always done together. If not, this point is moot.

I would make the regexp a bit more robust, though (here just the first rule as example):

Code:

sed "s/TA/AT/g" file

This will change every "TA" to "AT". But i fact you are interested only in changing the "TA" at the end of the line. This will also improve your code because accidental changes somewhere in the middle of a line can't happen any more. Therefore:

Code:

sed "s/TA$/AT/g" file

For the same reason you can drop the "g" option of the substitution: you want to change only one "TA" per line (the one immediately before the line end), hence:

Code:

sed "s/TA$/AT/" file

Finally, as long as it is possible you should enclose sed-expressions in single quotes instead of double quotes. In your special case it doesn't matter but some meta-characters are expanded within double-quotes whereas in single quotes nothing is expanded at all. Therefore, finally:

Code:

sed 's/TA$/AT/' file

One last tip: i usually write sed-scripts line per line, it is easier to read this way, IMHO:

Code:

sed 's/TA$/AT/
     s/TC$/CT/
     s/TG$/GT/
     s/GC$/CG/
     s/GA$/AG/
     s/CA$/AC/' file

I hope this helps.

bakunin