Perl script to calculate N50
By Poonam Mahapatra 2695 days ago
#! /usr/local/bin/perl5.8.3 -w
###
### Script Name : calcN50.pl
### Description : This script calculates the N50 of a collection of sequences in a fasta file
### Input : A fasta sequence file and the minimum length of sequence to consider it for the N50 calculation
### Output : None. The N50 value as well as the number of sequences >= this value is sent to STDOUT
###
use strict;
use Getopt::Long;
use Bio::SeqIO;
my $fasta_file;
my $filter_length;
GetOptions("fasta_file=s" => \$fasta_file, "length_filter=i" => \$filter_length);
die "Usage: $0 [options]
\t\t-f /path/to/fasta/file [Required]
\t\t-l filter seq less than length (0 if no filter is to be done)\n\n" if !$fasta_file || !defined($filter_length) || $filter_length !~ /\d+/;
###
### Get the length of each sequence:
###
my $in = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta');
my @seq_lengths = ();
while (my $seq_obj = $in->next_seq){
next if length($seq_obj->seq) < $filter_length;
push @seq_lengths, length($seq_obj->seq);
}
###
### Determine the N50:
###
my @vals;
my $sum = 0;
for my $val (@seq_lengths){
chomp $val;
$sum += $val;
push(@vals, $val);
}
my @sorted = sort { $a <=> $b } @vals;
my $runningSum = 0;
my $N50 = 0;
foreach my $v (@sorted)
{
$runningSum += $v;
if($runningSum >= ($sum / 2))
{
$N50 = $v;
last;
}
}
###
### Determine the number of sequences >= than the N50 in length:
###
my $count = 0;
foreach my $v (@sorted)
{
if($v >= $N50)
{
$count++;
}
}
printf("N50: $N50 Count >= N50: $count\n");
