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

2056360013       Musacgagchagshgashcgahcgacacsasasasacsacsasasacacaasc
+assacsaascascascascac
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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

Thanks for your help, but non of this things work even if i follow your instructions to the letter. Putting the if loop within the while loop only prints the ids and no sequences. Putting it in the big while loop prints several lines repeatedly