#!/usr/bin/perl -w
use strict;

my $ID = 1;
while (<DATA>)
{
   # this regex captures the trailing number if
   # the line starts with a ">"
   # the .*? means a "minimal match" of anything while 
   # allowing the rest of the regex to succeed.
   # the \n is counted as white space, a \s* character
   #
   if (my ($number) = $_ =~ /^>.*?(\d+)\s*$/)
   {
      print '>ID'.$ID++," $number\n"; 
   }
   else
   {
      print;
   }
}

=prints
>ID1 80
AGGGGGGGGGTTCCC
>ID2 85
TTTCCCGGGAAAA
>ID3 112
GGCCCCTTTGAGG
=cut

__DATA__
>Sample_1_x80
AGGGGGGGGGTTCCC
>Sample_2_x85
TTTCCCGGGAAAA
>sample_3_x112
GGCCCCTTTGAGG

##</code><code>##

while (<DATA>)
{
   if (my ($sample, $number) = $_ =~ /^>.*?(\d+).*?(\d+)\s*$/)
   {
      print '>ID'.$sample," $number\n"; 
   }
   else
   {
      print;
   }
}