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]

In reply to Re^4: How to format fasta file by andyBio
in thread How to format fasta file by andyBio

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