This is to test<X-REF REFID="FN001">1</X-REF> some more text. <FTN ID="FN001">Example111</FTN>

This is to test<X-REF REFID="FN002">2</X-REF> some more text. <FTN ID="FN002">Example222</FTN>

This is to test<X-REF REFID="FN003">3</X-REF> some more text. <FTN ID="FN003">Example333</FTN>

This is to test<X-REF REFID="FN001">1<FTN>Example111</FTN></X-REF> some more text.

This is to test<X-REF REFID="FN002">2<FTN>Example222</FTN></X-REF> some more text.

This is to test<X-REF REFID="FN003">3<FTN>Example333</FTN></X-REF> some more text.

open(IN, "<temp.in") || die "\n Can't open file\n $!\n";

open(OUT,">temp.out");

## Search for FTN

my %values;

while(<IN>) {

if(s/\<FTN ID\=\"FN(\d{3})\"\>(.+?)\<\/FTN\>/\<FTN$1\>/) {

$values{$1} = $2;

}

}

## replace X-REF

while(<IN>) {

s/(<X-REF REFID="FN(\d{3})">)(.+?)(<\/XREF>)/$1$values{$2}$3/;

print OUT;

}

close(IN);

close(OUT);

But i don't get any output in temp.out

In my input file X-REF occurs first and FTN occurs next. So my script is not working properly

Abigail-II is completely right about wasting time of others by not supplying the real example in the first place. Secondly, please use <code>-tags; they make code and input/output much more readable.
Anyways, the following should work for you:

#!perl

use strict;
use warnings;

open(IN, "<temp.in")  or die "Can't open file temp.in for input: $!\n"
+;
open(OUT,">temp.out") or die "Can't open file temp.out for output: $!\
+n";

for (<IN>) {
   s{<X-REF REFID="FN(\d+)">([^<]*)</X-REF>([^<]*)<FTN ID="FN\1">([^<]
++)</FTN>}
    {<X-REF REFID="FN$1">$2<FTN>$4</FTN></X-REF>$3};
   print OUT;
}
[download]

Hi, Sorry for not providing a proper example at first time. Thank you very much for your kind support. I receive compilation errors while using your code, since i am a new user, i really don't know how to debug. but the following code works fine and i get my required output. just share with you i have pasted the code i am using now.

open(IN, "<temp.in") || die "\n Can't open file\n $!\n";
open(OUT,">temp.out");

   ## Search for FTN
   my %values;

   # read through the input fileto get the values
   while(<IN>) {
      if(/<FTN ID="FN(\d{3})">(.+?)<\/FTN>/) { #no need to quote <, >,
+ ", =
         $values{$1} = $2;
      }
   }
   close(IN);

   open(IN, "<temp.in") || die "\n Can't open file\n $!\n";

    ## replace X-REF
    while(<IN> ) {
       s/<FTN.+?<\/FTN>//; # get rid of existing <FTN> tags - we alrea
+dy have the values from them
       s/(<X-REF REFID="FN(\d{3})">.*)(<\/X-REF>)/$1<FTN>$values{$2}<\
+/FTN>$3/; # alter the X-REF LINE
       print OUT;
    }

close(IN);
close(OUT);
[download]

Once again thanks for your support.

edited by ybiC: Replace opening <pre> tag with <code> as per Monastery convention *and* add closing tag for same

You know, it would really, really help if you post your real problem the first time around. Now I've wasted time answering a question that isn't your problem at all.

I'm not going to waste more time on you. One last hint: if you have exhausted your input in your first while loop, there isn't more input to read in the second loop.

Goodbye.

Abigail