You're right, some of these lines aren't doing what you think. next immediately breaks out of the current while loop and restarts the loop at the beginning, so the following line is never executed. That means it never tells you that $replace is undefined, so what you're trying to do with it won't work.

In general, when your text is arranged in multi-line chunks, it works best to process it that way rather than line-by-line. You can use the input record separator variable $/ to split your input file on something that ends each chunk. That way you don't have to dance around with saving each line long enough to look at the next line and see if something needs to be done to the previous line before outputting it.

Here's an example of what I'm talking about; you can adjust it to use your input and output files. It reads in each chunk, looks to see if it has the piece you want to copy, and copies it into the other spot if it's there.

#!/usr/bin/env perl
use strict; use warnings;

$/ = '/Hit_accession>';

while(<DATA>){
  if( m{<Hit_def>(.+?) odorant-bin} ){
    my $match = $1;
    s{(<Hit_id>).+?(</Hit_id>)}{$1$match$2};
  }
  print $_;
}

__DATA__
<Hit_num>6</Hit_num>
<Hit_id>gnl|BL_ORD_ID|3665984</Hit_id>
<Hit_def>gi|158703516|gb|ABW77886.1| odorant-bin...
<Hit_accession>3665984</Hit_accession>
<Hit_num>7</Hit_num>
<Hit_id>gnl|BL_ORE_ID|3665984</Hit_id>
<Hit_def>gi|153326716|gb|ABF88997.2| odorant-bin...
<Hit_accession>3665984</Hit_accession>
[download]

@ Anonymous monk, thanks for the links I'll be sure to study them.

@ Aaron B., thank you this has solved my problem beautifully.

I really think we (and perhaps, you) need a clearer definition of what you're trying to do... and what rule establishes that the "requirement is met?"

If it's a one-off replacement, done once, you can do it manually -- with an editor -- far more readily than with a script, regexen and an ill-speced appear to the Monks.

So, judging that what you've shown is one sample of multiple replacements you need to do, give us the rule for replacement: what does the "following line" have to contain (and what is NOT allowed in it) to justify replacing the preceding line?

A good spec makes it easy for us to help. Posting a poor, incomplete or inaccurate spec just leads to frustration, all around.

Just one additional remark on top of the previous posts.

Since you are opening this file for output, IN is a very poor choice of identifier.

nor do I know if my regular expression are correct

Would you like to find out? Here is how

use re 'debug';
$_ = q{<Hit_id>gnl|BL_ORD_ID|3665984</Hit_id>};
s/\>.\</\>REPLACE\</;
__END__
[download]

I don't think next is doing what I want

What is that (what do you want)? How did you learn about next?

See next, perlsyn, See "Loop control" section in Learn Perl in about 2 hours 30 minutes

See "Loop control" subsection in "Control Flow" section of Chapter 3 in the free book Modern Perl a loose description of how experienced and effective Perl 5 programmers work....You can learn this too.

So to learn about next you try like this

for my $ix (1..10){
    print "ix($ix)\n";
    if( $ix == 3 ){
        print "its threeee\n";
        next;
        print "PANCAKES\n";
    }
    print "its not threee\n";
}
__END__
[download]

After try the above two programs, what did you learn? What are you going to try next?