Use of uninitialized value $_ in scalar chomp at test.pl line 37.
Use of uninitialized value $_ in pattern match (m//) at test.pl line 3
+8.
Use of uninitialized value $_ in numeric gt (>) at test.pl line 39.
Use of uninitialized value $_ in numeric lt (<) at test.pl line 39.
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        chomp;
        next if /^>/;     # discard headers
        next if length($_) > 30 or length($_) < 15; # discard unwanted
+ sizes
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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.



Spirit of the Monastery

Andy, better change that '<DATA>' into '<STDIN>', then you can either:

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

Look Perlmonks is not a code writing service, we expect you to show efforts to learn programming.

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!

Cheers Rolf
_{(addicted to the Perl Programming Language and ☆☆☆☆ :)
Je suis Charlie!}

Hi andyBio,

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;
}
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And here is how I run it:

perl test.pl -a spe try.txt > result
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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.
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