use strict; 
use warnings; 
my $infile = "rep_set_ass_tax.fna";
my $outfile = "seq_id.txt";  # you need to open this only if writing to a file 

open(IN, "<", $infile) or die "Died!!"; 


while (my $line=<IN>) { 
  if($line=~/>\s*(\d+)/) {
     print $1 . "\n"; 
  } 
} 
close IN;