length_distribution.pl

#! /usr/bin/perl
use strict; use warnings;

# Get length distribution of sequences for any
# bioperl compatible format. Prints to STDOUT

use Bio::SeqIO;
use Number::Range;
use Getopt::Long;

my $file; # input file
my $format; #file format
my $help;
my $min; # minimum length
my $max; # maximum length
my $range; # stores range of sequence lengths to be analyzed
my @nt_len; # intermediate array for hash initialization
my %nt_len; # initiate hash to store sequence length counts 

if ( @ARGV != 8 || defined($help) ) 
{
	die <<END;
	##########################################
	This script outputs length distribution
	for any bioperl compatible format that
	contains primary sequence
	##########################################
	USAGE:
	perl length_distr.pl --in-file <file_name> --format <file_format> --min <INT> --max <INT>
END
} 

GetOptions(
            'in-file=s'  => \$file,
            'format=s'   => \$format,
            'min=i'      => \$min,
            'max=i'      => \$max,
            'help'       => \$help,
) or die "Incorrect usage!\n$help\n";

my $inseq = Bio::SeqIO->new(-file => "<$file",
                            -format => $format,);

$range = Number::Range->new( "$min..$max" );
my @numbers = $range->range;

foreach my $nt ( @numbers )
{
	push (@nt_len, $nt);
	push (@nt_len, 0);
}
%nt_len = @nt_len;
                            
while ( my $seq = $inseq->next_seq ) 
{
	my $length = $seq->length;
	$nt_len{$length}++;
}

foreach my $key ( sort {$a<=>$b} keys(%nt_len) ) 
{
	print "$key\t$nt_len{$key}\n";
}