Hey Dave. For the reverse complement the code will be something like this

my $raw=<IN>;
$rev= reverse $raw;
$rev=~tr/ATGCatgc/TACGtacg/;
[download]

my problem actually is doing this only to every other line and not the entire file

this is what i came up with, but it doesnt work

while(@inf=<IN>)
{
 if(i%2==1)
{
$inf[i]=reverse $inf[i];
}
}
[download]

In this i was just trying to find the reverse to see if this code performs the action on the lines I want it to.. but no luck. Im still thinking of any other way. Any suggestions?

variables in Perl need sigils, so it must be $i not just i

(using strict and warnings should have prevented you)

and you need to increment it with ++$i within the loop.

As an alternative you could just test $. % 2 since $. automatically holds the line-number.

Cheers Rolf

( addicted to the Perl Programming Language)

my problem actually is doing this only to every other line and not the entire file

The special variable $. (documented in perldoc perlvar) keeps count of the line numbers, so you can do something like:

while(<IN>) {
  next if $. % 2; # skip odd lines
  # do the processing
}
[download]

Cheers,
Rob