Hello andyBio,

It looks as though your first while loop constructs filename strings and prints them out; then, immediately before the second while loop, you want to open the last constructed filename for writing. If this is what you are doing, there are three problems:

(1) As Laurent_R says, $temp is out of scope by the time you try to use it in the open statement. To fix this, you need to give it a wider scope:

...
my $temp;        # declare $temp before the loop

while (...)
{
    ...
}

close FASTQIN;
my %count_seq;
open my $fh, ... # $temp is still in scope
...
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(2) The statement my $temp = print $head, $seq; doesn’t do what you want it to, because print returns a boolean value indicating whether the print operation was successful or not. You need something like this:

$temp = $head . $seq;
print $temp;
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(3) The first while loop’s condition may never be true, in which case $temp will never be initialized; so you should test for this possibility:

close FASTQIN;
my %count_seq;

if (defined $temp)
{
    open my $fh, '<:encoding(UTF-8)', $temp or die "Cannot open $temp 
+$!";

    while (<$fh>)
    {
        ...
    }
}
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Hope that helps,