Print a variable which is inside two loops - perl

Question

I couldn't figure it out how to escape this.
I would like to print the variable $rfam_column, which is inside two loops. But I cannot just write the print command right after the place where $rfam_column appears, because I would like to print other things which will be outside the loop and combine them to the printed content.
I would appreciate any advice as to what I'm doing wrong here.
use warnings;
use strict;
my $in;
GetOptions('input' => \$in) or die;
if ( $in ) {
my $input = $ARGV[0] or die;
open (my $fh, '<', $input) or die "Can't open $input $!\n";
chomp (my #db_file = <$fh>);
close $fh;
my #list = grep /RNA/, #db_file;
my $column;
my #column = ();
foreach $column ( #list ) {
my #all_columns = split (/\t/, $column);
my $rfam_column = $all_columns[0];
# insert "|" between RFs
foreach $_ ( $rfam_column ) {
s/^/|/;
}
}
}
print "$rfam_column";
Global symbol "$rfam_column" requires explicit package name at script_vbeta.pl line 90.
Execution of script_vbeta.pl aborted due to compilation errors.
EDITED to include all the code and information of the input--output as suggested:
Input file is a table with n lines vs n columns like this (I extracted a few columns otherwise it would be much long to represent in a line):
RF00001 1302 5S ribosomal RNA
RF00006 1307 Vault RNA
RF00007 1308 U12 minor spliceosomal RNA
RF00008 1309 Hammerhead ribozyme (type III)
Output should be like this:
|RF00001|RF00006|RF00007
And the code (usage: script.pl -i input_file):
use warnings;
use strict;
use Getopt::Long;
Getopt::Long::Configure("pass_through");
my $in;
GetOptions('input' => \$in) or die;
if ( $in ) {
my $input = $ARGV[0] or die;
open (my $fh, '<', $input) or die "Can't open $input $!\n";
chomp (my #db_file = <$fh>);
close $fh;
my #list = grep /RNA/, #db_file;
my $column;
my #column = ();
foreach $column ( #list ) {
my #all_columns = split (/\t/, $column);
my $rfam_column = $all_columns[0];
# insert "|" between RFs
foreach $_ ( $rfam_column ) {
s/^/|/;
}
}
}
print "$rfam_column";

Answer 1

I think you want
if ($in) {
...
my #rfams;
for my $row (#list) {
my #fields = split(/\t/, $row);
my $rfam = $fields[0];
push #rfams, $rfam;
}
my $rfams = join('|', #rfams);
print("$rfams\n");
}

Answer 2

I would like to print other things which will be outside the loop and combine them to the $rfam_column content
You can include anything that is in an outer scope in print. You can just put your print statement inside the inner loop
By the way, I don't know what you mean by
# insert "|" between RFs
foreach $_ ($rfam_column) {
s/^/|/;
}
That is the same as
$rfam_column =~ s/^/|/;
which just adds a pipe | character to the beginning of the string
What is an RF?