As moritz said, 1 (or ++) is a common choice of value, but it's not necessarily the best one. It doesn't usually matter these days for 100k elements, but it's better (thanks, Liz! ;) for memory size to do something like this:

my ($undef);
while (whatever...) {
    ....
    $hash{$key} = $undef;
}
[download]

This way each element points to the same $undef value. Otherwise, each element would point to a different copy of the value 1. That's a kind of "poor man's aliasing". For bonus points, you might look at Array::RefElem or Data::Alias.

I have changed the code, but now my problem seems to be that I can only access the last line of the output outside the loops. I wonder if there's a way to store the variables inside the loop to be accessible outside. The code looks like this now.

if(@ARGV < 3){
die "Not enough arguments\n";
}
$sequence="";
$fastaID;
open(FILE1,"$ARGV[0]") or die "No fasta file provided in command line:
+ $!\n";
while ($line=<FILE1>){
chomp($line);
if ($line=~/^\s*$/){
next;
}elsif ($line=~/^.*$/){
$fastaID=$line;
$fastahash{$fastaID}=1;
}
}
open(FILE2,"$ARGV[2]") or die "No fasta file provided in command line:
+ $!\n";
while($line2=<FILE2>){
chomp($line2);
if ($line2=~/^>/){
@data=split(" ",$line2);

$fasta=$data[1];

$sequence="";
}else{
$sequence.=$line2;
}
}
if (exists $fastahash{$fasta}){
print "$fastaID\t $sequence\n";
}


exit;
[download]

And the output, which is just the last key value in the fastahash is

2056360013       Musacgagchagshgashcgahcgacacsasasasacsacsasasacacaasc
+assacsaascascascascac
[download]

Sadly you ignored half of my advice; it wasn't given without reason. Please reconsider your position.

You print can only be executed once because it's not inside a loop (should be inside the while loop). Proper indention would have made that obvious, and use strict would have told you that $fasta isn't in scope in the if (exists $fastahash{$fasta}) (if you would have declared it properly inside the while loop).

Perl 6 - second systems done right