You can use this code..,

use strict;
use warnings;
use Data::Dumper;
my($File,$FILE_FH,$data,@total_data,$new,@gi);
$File="./fasta.txt";
open  $FILE_FH, '<', $File or die "Failed to Open File $File for $!";
 $data=<$FILE_FH>;
 @total_data=split(/gi\|(\d+)\|/,$data);
foreach $new(@total_data)
{
    push @gi,$new if($new =~ /^\d+$/);
}
print Dumper @gi;
[download]