There is no need to substitute anything. Capture what is necessary and re-format the ">" line.
No need to be overly tricky when a couple of straight-forward lines of code will do. 
#!/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

[download]
Well, if you want to get the sample number from the ">" line then: 
while (<DATA>)
{
   if (my ($sample, $number) = $_ =~ /^>.*?(\d+).*?(\d+)\s*$/)
   {
      print '>ID'.$sample," $number\n"; 
   }
   else
   {
      print;
   }
}

[download]
which will print the same thing

In reply to Re: modifying a file with regex! by Marshall
in thread modifying a file with regex! by rna_follower

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