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

In reply to Re^3: find reverse complement of every 2nd line by syphilis
in thread find reverse complement of every 2nd line by bingalee

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