Shell Programming and Scripting

Hi,
I have a string of letters that are upper and lower case. I would like to replace all the lowercase letters with N. Also, there are only 4 letters, so it may be easier to replace each lower case letter with N. Either way, I do not know know to do this.

Example line

ATGACTGtagctagATGCTgtg

I want it to be

ATGACTGNNNNNNNATGCTNNN

The lowercase letters are a g c t.

Thanks so much for any help!

Mike

echo "ATGACTGtagctagATGCTgtg" |sed 's/[a-z]/N/g'


Best Regards,
Suresh...

Code:

echo ATGACTGtagctagATGCTgtg |tr "[a-z]" "N"

Code:

echo "ATGACTGtagctagATGCTgtg" |sed 'y/tagc/NNNN/'
ATGACTGNNNNNNNATGCTNNN

A common misconception. It appears that it works because usually there's not `[' or `]' in the given string, but it is translating those as well.
You can prove it to yourself by checking the result of this:

Code:

echo AT[GACTGtagctagATGCTgtg |tr "[a-z]" "N"

# output
ATNGACTGNNNNNNNATGCTNNN

Also for the sake of locale, it is best to use a character class set

Code:

echo ATGACTGtagctagATGCTgtg | tr '[:lower:]' 'N'

And for the sake of portability, both character arrays should be of the same length.

Code:

tr '[:lower:]' '[N*]'

or for this specific case

Code:

tr acgt '[N*4]'

or

Code:

tr acgt NNNN

Regards,
Alister

Code:

 $ echo "ATGACTGtagctagATGCTgtg" | ruby -e 'print gets.gsub(/[a-z]/,"N")'