#!/usr/bin/perl
use warnings;
use strict;
use v5.14;

use Bio::PopGen::IO;
use Bio::PopGen::Statistics;

open my $out_file, ">", "chr22_exome_snps_processed_AMR_TRUNCATED_STATS"
  or die "Can't open output file: $!\n";

my $io = new Bio::PopGen::IO(
    -format => 'csv',
    -file   => "chr22_exome_snps_processed_AMR_TRUNCATED"
);

my @markers;
my @samples;
while ( my $ind = $io->next_individual ) {
    if ( $ind =~ /^SAMPLE/ ) {
        push @markers, $ind;
    }
    else {
        push @samples, [$ind];
    }
}

my $segsites   = Bio::PopGen::Statistics->segregating_sites_count( \@samples );
my $singletons = Bio::PopGen::Statistics->singleton_count( \@samples );
my $pi         = Bio::PopGen::Statistics->pi( \@samples );
my $theta      = Bio::PopGen::Statistics->theta( \@samples );
my $tajima_D   = Bio::PopGen::Statistics->tajima_D( \@samples );
my $D_star     = Bio::PopGen::Statistics->fu_and_li_D_star( \@samples );
my $F_star     = Bio::PopGen::Statistics->fu_and_li_F_star( \@samples );

say $out_file "Population: AMR\tChromosome: 22_TRUNCATED";
say $out_file
  "Seg sites\tSingletons\tPi\tTheta\tTajima's D\tFu & Li F*\tFu & Li D*";
say $out_file
  "$segsites\t$singletons\t$pi\t$theta\t$tajima_D\t$F_star\t$D_star";


##</code><code>##

Can't call method "isa" on unblessed reference at /usr/local/share/perl/5.14.2/Bio/PopGen/Statistics.pm line 901, <GEN0> line 3