use strict;
use warnings;

while (<DATA>) {
    s/a/x/g unless $. & 1;
    print;
}

__DATA__
Anyone know a way to apply a
substitution in a file to every
other line rather
than the hole file?
[download]

Prints:

Anyone know a way to apply a
substitution in x file to every
other line rather
thxn the hole file?
[download]

perl -i.bak -nle 's/search/replace/g unless $. & 2; print' file(s)
[download]

The above will apply the changes in line numbers 1,3,5,7,......

perl -i.bak -nle 's/search/replace/g unless $. & 1; print' file(s)
[download]

The above will apply the changes in line numbers 2,4,6,8,......

NOTE: Based on the idea from Re: Search and replace in all odd lines by GrandFather

perl -i.bak -nle 's/search/replace/g unless $. & 2; print' file

Your one-liner is not going to do what you think. $. & 2 is going to evaluate to true whenever the third second bit from the right (2 is binary 100) is set. Given this input file (lines.txt)

line 1
line 2
line 3
line 4
line 5
line 6
line 7
line 8
line 9
[download]

adapting your one-liner to just print the lines gives

$ perl -nle 'print unless $. & 2;' lines.txt
line 1
line 4
line 5
line 8
line 9
[download]

Did you actually test your adaptation of GrandFather's idea before posting? Changing between odd and even is as simple as if $. & 1 and unless $. & 1. Perhaps you could have a look at "Bitwise And" in perlop to further your understanding.

Cheers,

JohnGG

Update: Corrected typo.

Update 2: Corrected huge balls-up, thanks fenLisesi. Where did I get "2 is binary 100" from?

Update 3: And thanks clinton, saw your reply after /msg from fenLisesi

If you want to modify all the odd lines of the file in place you can use something like:

perl -i.bk -lne 's/foo/bar/g if $.%2;print;' foo.txt
[download]

This will substitute all the foo's into bar's that appears in odd lines of the file foo.txt (saving a backup of the original file in foo.txt.bk)

Hope this helps

citromatik

Here's what I mean (the first line uses bash to set up the test case...)

for i in 1 2 3 4 5; do perl -e'print "$_\n" foreach 1..$ARGV[0]' $i > 
+$i;done
[download]

perl -ne'printf "File: $ARGV \$.: %2d real line: $_",$. if $. & 1' 1 2
+ 3 4 5
[download]

File: 1 $.:  1 : real line: 1
File: 2 $.:  3 : real line: 2
File: 3 $.:  5 : real line: 2
File: 4 $.:  7 : real line: 1
File: 4 $.:  9 : real line: 3
File: 5 $.: 11 : real line: 1
File: 5 $.: 13 : real line: 3
File: 5 $.: 15 : real line: 5
[download]

Fun, eh? :)