#!/usr/bin/perl
use strict;
use warnings;
use Text::Table;
use Sort::Naturally;

my %data;
my @col2 = qw/ PA TT AT /;

while (<DATA>) {
	chomp;
	my ($name, $col2, $col3) = split /\t/;
	push @{ $data{$name}{$col2} }, $col3;
}

my $tb = Text::Table->new( map {title => $_}, @col2);

for my $name (nsort keys %data) {
	my @tmp;
	local $" = ',';
	for my $col2 (@col2) {
		push @tmp, $data{$name}{$col2} ?
			"@{ $data{$name}{$col2} }" :
			"";
	}
	$tb->load(\@tmp);
}

print $tb;

__DATA__
Name_1	TT	XL_927799.1
Name_1	PA	PA_392
Name_1	AT	ZX_003039195.1
Name_2	TT	XL_931313.1
Name_2	AT	ZX_003043016.1
Name_3	TT	XL_929616.1
Name_3	PA	PA_5040
Name_3	PA	PA_6336
Name_4	TT	XL_928294.1
Name_4	PA	PA_917