Assisting: both errors appear to refer to a lack of content in $_ the default variable set by various operations. $_ is explicitly mentioned in your line 3 and implicit in your line 2.

Inserting a print $_\n before the chomp will probably confirm or rebut my hypothesis. Then, if I'm on target, you can read up to find what you expected to set the default.

Windows:

type fasta.txt | perl laurent_example.pl

Unix:

cat fasta.txt | perl laurent_example.pl

And to get rid of your current error, just add this line after the chomp;

next if($_=~/^\s*$/);

Hint: check on how to open a file instead of reading appended data like in Laurent's demonstration

update

... and/or avoid empty lines after __DATA__ if you are REALLY only running the demo code!

the program I posted did not have any of the errors or warnings that you report. This most probably means that the error is somewhere in the changes you made to the code.

Although I have some ideas on what might be wrong in your program (along the hints supplied by other monks), we can't fix a program that we don't see. The only way we can help you is if you show the code you're now using, with the changes you made.

Thanks a lot, Laurent R. Here is my complete code:

#!/usr/bin/perl -w

use strict;
use warnings;

my $num_args = @ARGV;
if ($num_args != 3) {
   
 print "\nUsage: $0 (-q|-a) <species> <input.(fq|fa)>";
 print "\nUse -q for fastq and -a for fasta files";
   exit;
   }

my $key=$ARGV[0];
my $species=$ARGV[1];
my $input=$ARGV[2];


if ($key ne "-q" && $key ne "-a"){
    print "Unexpected option: $key, use -q or -a.\n";
    exit;
}

if($key eq "-q")
{
    print "Option q was selected.\n";
    exit;
}

elsif( $key eq "-a" )
{
    print "Option a was selected.\n";
    
    my %count_seq;
    open(my $fh, '<:encoding(UTF-8)', $input);
    while ($fh) { 
        chomp;
        next if /^>/;                        # discard headers
        next if length($_) > 30 or length($_) < 15; # discard unwanted
+ sizes
        $count_seq{$_}++;                  # count occurrences
}
print "$_\t$count_seq{$_}\n" for keys %count_seq;
    exit;
}
[download]

And here is how I run it:

perl test.pl -a spe try.txt > result
[download]

It accepts either -q or -a as options. The error I get is this:

Use of uninitialized value $_ in scalar chomp at test.pl line 39.
Use of uninitialized value $_ in pattern match (m//) at test.pl line 4
+0.
Use of uninitialized value $_ in numeric gt (>) at test.pl line 41.
[download]

Hi andyBio,

try to change these two lines:

    open(my $fh, '<:encoding(UTF-8)', $input);
    while ($fh) {
[download]

as follows:

    open my $fh, '<:encoding(UTF-8)', $input or die "Cannot open $inpu
+t $!";
    while (<$fh>) {
[download]

The main change is on the while line (the (<$fh>) part), but checking whether the program could open the file is also essential.

A few more things could be improved, but the above corrections should get you where you want.