General :: Sed: Perform Replacement Only On Even-numbered Lines?
Jul 20, 2010
I'm sure this is possible but I can't figure it out. I have a file formatted like this:
Code:
>SEQUENCE1
FGFD665:?@663:BBBBAA?A@<<4!1004699<7444399>???888455555?AAA?AABBB@@@<<<34
>SEQUENCE2
>&<4!1004699<7444399>???888455555?AAA?AABBB@@@<<<34BBB@@
>SEQUENCE3
???888455555?AAA?AABBB@@@<<<341004699<7444399>???888BBB@@
The odd-numbered lines containing >SEQUENCE# are the headers and the even-numbered lines containing a variety of characters represent DNA sequence read quality scores.
I want to replace all of the greater-than (">") symbols in the quality scores (even-numbered lines) with a "0" but I want to leave the greater-than symbols on the odd-numbered lines alone. I would just use sed -i '/^>/! s/>/0/g' $FileName but sometimes the quality scores begin with a ">" as well.
I'm sure there is a simple modification of a normal sed command with an "n" inserted somewhere but I can't figure it out.
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May 28, 2010
I'm looking for a command to swap the even/odd numbered lines in a file. Example input file:
Code:
1
2
3
4
[code]...
Example output file:
Code:
2
1
4
3
[code]....
I'm sure there's a way to do it with sed, awk, grep and the like but it's been many years since I've used these commands on a daily basis and I can't seem to figure out the correct syntax.
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