while(
defined(my $head = <FASTQIN>) &&     
defined(my $seq = <FASTQIN>) &&      
defined(my $qhead = <FASTQIN>) &&    
defined(my $quality = <FASTQIN>)     
){
  substr($head, 0, 1, '>'); 
  my $temp = print $head, $seq;
}
  close (FASTQIN);  

my %count_seq;
    open my $fh, '<:encoding(UTF-8)', $temp or die "Cannot open $temp 
+$!";
    while (<$fh>) { 
        chomp;
        next if /^>/;                        
        next if length($_) > 30 or length($_) < 15; 
        $count_seq{$_}++;                  
    }
[download]

Use of uninitialized value $temp in open at test.pl line 44.
Use of uninitialized value $temp in concatenation (.) or string at tes
+t.pl line 44.
Cannot open  No such file or directory at test.pl line 44.
[download]

open my $fh, '<:encoding(UTF-8)', $temp or die "Cannot open $temp $!";
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We don't know what your code looks like now, so we don't know where and how you're using the $temp variable, but if it was declared within the while loop, then it no longer exists once the while loop is completed.

So you could just declare a new my $temp; variable there (although, since you ask the question, these things are probably not entirely clear to you, you might as well use another variable name for clarity).

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>)
    {
        ...
    }
}
[download]

Hope that helps,

Athanasius <°(((>< contra mundum

Iustus alius egestas vitae, eros Piratica,