Hello perl_beginner,

Thank you for asking good question, please keep it up. Coming to your requirement now, off course SHELL can't understand you BOLD characters(which you actually made for us to understand) so considering that you character/characters N will come in a continuous sequence only, following may help you in same.

Code:

awk '{split("ATC:C:TCGCG:G", array,":");$(NF+1)=$1;sub(/N*N/,array[NR],$NF);print}'   Input_file

Output will be as follows.

Code:

CGGCGCCTCGCNNNCGAGCG CGGCGCGCCGAATCCGTGCG CGGCGCCTCGCATCCGAGCG
TCGCNGC GCGCCGC TCGCCGC
ACGGCNNNNN ACGGCCTCGCG ACGGCTCGCG
CGGCNGCCCGCCC CGGCGCGCCGTCC CGGCGGCCCGCCC

Here you need to give you all strings which you want to be substituted(in newly created 3rd column) in split("ATC:C:TCGCG:G", array,":") highlighted column of split according to their sequence/line vice and it should fly then. If you have more permutations/combinations for this please do let us know on same then.

EDIT: We could put splitcode into BEGIN section so that array will be created only once. As follows a minor change in above code.

Code:

awk 'BEGIN{split("ATC:C:TCGCG:G", array,":")};{$(NF+1)=$1;sub(/N*N/,array[NR],$NF);print}'  Input_file

Thanks,
R. Singh