text-processing sed – Write a sed One-Liner to Add Character After Every Third Character

sedtext processing

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?

Best Answer

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/+$//'

Related Solutions

Sed or tr one-liner to delete all numeric digits

To remove all digits, here are a few possibilities:

tr -d 0-9 <old.txt >new.txt
tr -d '[:digit:]' <old.txt >new.txt
sed -e 's/[0-9]//g' <old.txt >new.txt

If you just want to get rid of the page numbers, there's probably a better regexp you can use, to recognize just those digits that are page numbers. For example, if the page numbers are always alone on a line except for whitespace, the following command will delete just the lines containing nothing but a number surrounded by whitespace:

sed -e '/^ *[0-9]\+ *$/d' <old.txt >new.txt

(\+ is a GNU extension; with some sed implementations, you may need the longer standard alternative: \{1,\} or use [0-9][0-9]*).

You don't need to use the command line for this, though. Any halfway decent editor has regexp search and replacement capabilities.

Substituting strings in a very large file

With awk you can avoid reading huge amount of text at once:

awk -vRS='http://' -vORS='\nhttp://' 1 urls.txt > urlsperline.txt

The success may depend on the used awk implementation. For example gawk works fine, but mawk crashes.

Best Answer

Related Solutions

Sed or tr one-liner to delete all numeric digits

Substituting strings in a very large file

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