How do I write a sed one-liner to add a character after every third character?

Question

So, I have a string that looks like this:

AUGGCCAUGGCGCCCAGAACUGAGAUCAAUAGUACCCGUAUUAACGGGUGA

And I want to split the string into 3-character chunks delimited by a '+' sign.

AUG+GCC+AUG+GCG+CCC+AGA+ACU+GAG+AUC+AAU+AGU+ACC+CGU+AUU+AAC+GGG+UGA

And I want to do that with my good friend sed.

I tried

cat codons | sed -r 's/([A-Z]\{3\})/\1\+/g'

...with no success.

What sed command can I use?

Answer 1

Since you don't want a trailing +, you could do:

fold -w3 | paste -sd+ -

That is, fold the lines on 3 character width, and paste those 3 character lines with themselves with + as the delimiter which in effect is like changing every newline character but the last one into a +. If the input had more than one line, you'll end up with those lines joined with a + which may or may not be what you want.

If you do need it to be sed, you can remove the trailing + after:

sed 's/.../&+/g;s/+$//'

Answer 2

sed 's/.../&+/g'

to get your way working you don't need to escape {} symbols:

sed -r 's/([A-Z]{3})/\1+/g'

Answer 3

This might work for you (GNU sed):

sed 's/...\B/&+/g' file

Answer 4

If sed is not a must using Ruby might be an alternative. The Ruby interpreter, ruby, can be used like sed and awk by running it with the -n option which makes it iterate over its input. The interpreter can then be feed with a Ruby one-liner by adding it as an argument to the -e option (which tells the interpreter to interpret the argument of -e rather than looking for a script in a file).

For this particular problem you can use the following one-liner (adapted from http://stackoverflow.com/a/3184271/789593):

ruby -ne 'puts $_.scan(/.{3}|.+/).join("+")'

In plain language it

• matches any 3 characters or at least one character, scan(/.{3}|.+/), in the input string, $_ (in this case the input is expected to come from standard in) and puts each match in an array,
• joins the array into a string with a '+' connecting each element, join("+"),
• and prints it terminated by a newline puts.

For example

echo "AUGGCCAUGGCGCCCAGAACUGAGAUCAAUAGUACCCGUAUUAACGGGUG" | ruby -ne 'puts $_.scan(/.{3}|.+/).join("+")'
AUG+GCC+AUG+GCG+CCC+AGA+ACU+GAG+AUC+AAU+AGU+ACC+CGU+AUU+AAC+GGG+UG

Note that it does not add any trailing '+'.