Assuming your text is stored in $_, you can do it in two lines. First line grabs the YYY info, second line substitutes the XXX. You may have to tweak the regexes depending on the precise specification.

    my %data = m!<X-REF REFID="([^"]+)">([^<]+)</XREF>!g;
    s!<FTN ID="([^"]+)">[^<]+</FTN>!<FTN ID="$1">$data{$1}</FTN>!g;
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Abigail

That is not an example, it is the actual content which i have to change.

now I am using the following code, but no output in temp.out.

open(IN, "<$file_name_xml") || die "\n Can't open file\n $!\n";
open(OUT,">temp.out");
while(<IN>)
{
    my %data = m#<X-REF REFID="([^"]+)">([^<]+)</XREF>#g;
    s#<FTN ID="([^"]+)">[^<]+</FTN>#<FTN ID="$1">$data{$1}</FTN>#g;
    print OUT $data;
}
close(IN);
close(OUT);
[download]

That is not an example, it is the actual content which i have to change

Really? It's just "YYY" that you have to replace with "XXX"? Just those three time the letter "Y"? And your tags are always X-REF followed by exactly a space, then REFID, then a =, then a ", etc? No spaces around the =, no single quotes? Good, then my regexes don't need any work!

print OUT $data;
[download]

Why are you printing $data? What's in that?

Furthermore, if you read in the file line by line, you will only do the substitution if both the X-REF and the corresponding FTN are on the same line.

Abigail

You assign to %data and print $data.

--
TTTATCGGTCGTTATATAGATGTTTGCA