>ENSCAPT00000000001.1 cdna (...)
CACTCCGCCGGCAAGGCCACCAAGTATCTGAAGGATGTCACGTTAAAGAAGCAATGTGTG
CCATTCCGGCGTTACAATGGTGGAGTTGGAAGGTGTGCCCAGGCCAAACAATGGGGCTGG
ACCCAGGGTCGGTGGCCCAAAAAGAGTGCTGAATTTTTGCTGCAC
>ENSCAPT00000000002.1 cdna (...)
CAGCTGCTGAAGACGGAGCTGGGGTCCTTCTTCACCGAGTACCTGCAGAACCAGCTGCTG
ACCAAAGGCATGGTGATCCTTCGGGACAAGATCCGCTTCTATGAGGGACAGAAACTGCTG
GACTCGCTGGCAGAGACCTGGGACTTCTTCTTCAGCGACGTGCTGCCCACGCTGCAGGCC
ATCTTCTACCC
>ENSCAPT00000000004.1 cdna (...)
ATGATGCTGGGAGAAGATGATGAGGAGTTCGTGGTGAAGGTGCGGGGTTTGCCTTGGTCC
TGCTCGGCTGACGAGGTGCAGCGGTTCTTCTCCGACTGCAAAATTCAAAATGGTGCTCAA
GGTATTTGTTTCATCTACACCAGAGAAGGCAGACCGAGTGGCGAGGCTTTTGTTGAACTT
GAATCCGAAGATGAAGTCAAACTATCAAACAACGTTGAAATGGATTGGGTGTTGAAGCAT
ACTGGTCCAAATAGTCCTGACACGGCCAATGATGGCTTTGTACGGCTTAGAGAACTCCCC
TTTGGATGTAGCA

##</code><code>##

#Open data file;
chomp($paths[1]);
my ($sfile) = $paths[1].$ARGV[0];
open my $fain,'<', $sfile
    or die "Unable to open $sfile\nError: $!\n";

my $length = $paths[3];
my $line = 0;
my %count;
while (my $fasta = <$fain>){
    
    if ($fasta !~ m/^>/){
                while ($fasta =~ /(.{$length})/g) {
                $count{$1}++;
                }
    }
    
    if ($fasta =~ m/^>/){
        #Print ID line
            print "$_ $count{$_}\n" for sort keys %count;
            %count = ();
            $line++;
            chomp($fasta);
            print "$line|$fasta\n";
    }
}
print "$_ $count{$_}\n" for sort keys %count;

##</code><code>##

#!/usr/bin/env perl -l

use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        $_ = substr $_, 1 if $. == 1;
        chomp;
        my ($key, @seq_parts) = split /\n/;
        print "KEY=|$key|";
        my $seq = join '', @seq_parts;
        print "SEQ=|$seq|";
    }
} 

__DATA__
>ENSCAPT00000000001.1 cdna (...)
CACTCCGCCGGCAAGGCCACCAAGTATCTGAAGGATGTCACGTTAAAGAAGCAATGTGTG
CCATTCCGGCGTTACAATGGTGGAGTTGGAAGGTGTGCCCAGGCCAAACAATGGGGCTGG
ACCCAGGGTCGGTGGCCCAAAAAGAGTGCTGAATTTTTGCTGCAC
>ENSCAPT00000000002.1 cdna (...)
CAGCTGCTGAAGACGGAGCTGGGGTCCTTCTTCACCGAGTACCTGCAGAACCAGCTGCTG
ACCAAAGGCATGGTGATCCTTCGGGACAAGATCCGCTTCTATGAGGGACAGAAACTGCTG
GACTCGCTGGCAGAGACCTGGGACTTCTTCTTCAGCGACGTGCTGCCCACGCTGCAGGCC
ATCTTCTACCC
>ENSCAPT00000000004.1 cdna (...)
ATGATGCTGGGAGAAGATGATGAGGAGTTCGTGGTGAAGGTGCGGGGTTTGCCTTGGTCC
TGCTCGGCTGACGAGGTGCAGCGGTTCTTCTCCGACTGCAAAATTCAAAATGGTGCTCAA
GGTATTTGTTTCATCTACACCAGAGAAGGCAGACCGAGTGGCGAGGCTTTTGTTGAACTT
GAATCCGAAGATGAAGTCAAACTATCAAACAACGTTGAAATGGATTGGGTGTTGAAGCAT
ACTGGTCCAAATAGTCCTGACACGGCCAATGATGGCTTTGTACGGCTTAGAGAACTCCCC
TTTGGATGTAGCA

##</code><code>##

KEY=|ENSCAPT00000000001.1 cdna (...)|
SEQ=|CACTCCGCCGGCAAGGCCACCAAGTATCTGAAGGATGTCACGTTAAAGAAGCAATGTGTGCCATTCCGGCGTTACAATGGTGGAGTTGGAAGGTGTGCCCAGGCCAAACAATGGGGCTGGACCCAGGGTCGGTGGCCCAAAAAGAGTGCTGAATTTTTGCTGCAC|
KEY=|ENSCAPT00000000002.1 cdna (...)|
SEQ=|CAGCTGCTGAAGACGGAGCTGGGGTCCTTCTTCACCGAGTACCTGCAGAACCAGCTGCTGACCAAAGGCATGGTGATCCTTCGGGACAAGATCCGCTTCTATGAGGGACAGAAACTGCTGGACTCGCTGGCAGAGACCTGGGACTTCTTCTTCAGCGACGTGCTGCCCACGCTGCAGGCCATCTTCTACCC|
KEY=|ENSCAPT00000000004.1 cdna (...)|
SEQ=|ATGATGCTGGGAGAAGATGATGAGGAGTTCGTGGTGAAGGTGCGGGGTTTGCCTTGGTCCTGCTCGGCTGACGAGGTGCAGCGGTTCTTCTCCGACTGCAAAATTCAAAATGGTGCTCAAGGTATTTGTTTCATCTACACCAGAGAAGGCAGACCGAGTGGCGAGGCTTTTGTTGAACTTGAATCCGAAGATGAAGTCAAACTATCAAACAACGTTGAAATGGATTGGGTGTTGAAGCATACTGGTCCAAATAGTCCTGACACGGCCAATGATGGCTTTGTACGGCTTAGAGAACTCCCCTTTGGATGTAGCA|

##</code><code>##

%count = ();