Re^2: Manipulating tab delimited file

Hello, Monks! Please, one more question. I didn't think I should start a new thread for this.

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; 
        $count_seq{$_}++;                  
    }
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this is a section of code I am trying to write. Is there a way to make the variable my $temp that was used in the while loop also available in the open filehandle statement? The code works OK till close (FASTQIN);. the error reads:

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.
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Line 44 is this:

open my $fh, '<:encoding(UTF-8)', $temp or die "Cannot open $temp $!";
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Kindly advise, monks! Thanks!

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Re^3: Manipulating tab delimited file
by Laurent_R (Canon) on Apr 29, 2016 at 06:25 UTC

$temp

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).

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Re^3: Manipulating tab delimited file
by Athanasius (Archbishop) on Apr 30, 2016 at 06:11 UTC

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,

Athanasius <°(((>< contra mundum Iustus alius egestas vitae, eros Piratica,

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