you should really put your code in <code></code> tags. But from what I can see your code looks like this(more or less):

 open in, "rep_set_ass_tax.fna"; 
 
 while ($line=<in>) { 
   if($line=~/>/) {
 
    @vettore=split(/\s+/, $line); 
    open my $fh, ">>seq_id.txt" or die "Cannot open output.txt: $!"; #
+ There is no need to open a file each time you need to print somethin
+g into it if it is the same file. just open it once before the loop a
+nd print to it 
    foreach (@vettore); # What is a loop and what is a proper way to w
+rite one. So you started a loop and what are you going to do with it(
+I mean variables in the loop)
      print $_ . "\n"; # OK, so you want to print something, but where
+ to STDOUT or into a file that you have opened
    close my $fh; # again my doesn't have any effect if use strict is 
+not called.
    } 
 }
[download]

First of all try to use strict and warnings, you will get a lot of info about your errors. Second, you have a some syntax errors(see comments in the above code). I I were you I would do something like this

use strict;
use warnings;

open(IN, "<", "rep_set_ass_tax.fna") or die "Died!!"; 
open (OUT , ">","seq_id.txt") or die "Cannot open output.txt: $!";
 while (my $line=<IN>) { 
   if($line=~/>/) {
 
      my @vettore=split(" ", $line); 
    
      foreach (@vettore){ 
       print OUT $_ . "\n"; 
      }
   } 
 }
 
 close IN;
 close OUT;
[download]

now this maybe is not exactly what you need to do but it will get you started

Cheers

UPDATE:

use strict;
use warnings;

open(IN, "<", "rep_set_ass_tax.fna") or die "Died!!"; 

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

UPDATE 2: Did you manage to get it working?? Also is this a fasta file orreally a one line file "> 1 ATTTAAA..."??? it is a bit strange if it is a one liner. usually those files look like this:

>1
ATGT...
>2
ATGGTGC..
[download]

also is there a space between > and 1? so you did several things wrong down there: it should look like this:

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

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


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

and use the code tags like:

<code>
My code;
</code>

baxy

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