#!/usr/bin/perl -w
use strict;

use Text::CSV_XS;

open (my $FILE1, '<', "file1.csv") or die "cannot open file1 $!\n";
open (my $FILE2, '<', "file2.csv") or die "cannot open file3 $!\n";
open (my $FILE3, '>', "file3.csv") or die "cannot open file3 $!\n";

my $csv = Text::CSV_XS->new ({ binary => 1, eol => $/ , 
                               sep_char => "\t", always_quote =>1});

print $FILE3 "Match\t".<$FILE1>; # header for file3
<$FILE2>;                        # skip header line of file2

my %file1; 
my %file2;

while (my $row = $csv->getline($FILE1)) 
{
    my @fields = @$row;
    my $id = $fields[4];
    $file1{$id}=["",@fields];
}

while (my $row = $csv->getline($FILE2)) 
{
    my @fields = @$row;
    my $id = $fields[0];
    $file2{$id}=["","","","","",@fields,"","","","",""];
}

foreach my $id1 (keys %file1)
{
    if (exists $file2{$id1})
    {
        $file1{$id1}[0] ="both";             #both files
        $csv->print ($FILE3, $file1{$id1});
    }
    else
    {
        $file1{$id1}[0] ="1";                #file1 only
        $csv->print ($FILE3, $file1{$id1});
    }
}

foreach my $id2 (keys %file2)
{
    if (!exists $file1{$id2})
    {
        $file2{$id2}[0] ="2";               #file2 only
        $csv->print ($FILE3, $file2{$id2});
    }
}

##</code><code>##

Group	Functional_Category	LT	IA	ID	Symbol	Description	TID	GID	LO	S1	S2	HL	Status	V1	V2	IN 
q	w	a	a	1	AA	some description	10	11	1	s1a	s2a	1	1	1	1	1
q	w	b	b	2	BB	another descrp	11	12	1	s1b	s2b	1	1	1	1	1
q	w	c	c	5	CC	despript A	12	13	1	s1c	s2c	1	1	1	1	1

##</code><code>##

ID	Symbol	Description	TID	GID	LO	S1	S2 
2	BB	another descrp	11	12	1	s1b	s2b
4	DD	some more stuff	14	14	4	s1d	s2d

##</code><code>##

Match	Group	Functional_Category	LT	IA	ID	Symbol	Description	TID	GID	LO	S1	S2	HL	Status	V1	V2	IN 
"1"	"q"	"w"	"a"	"a"	"1"	"AA"	"some description"	"10"	"11"	"1"	"s1a"	"s2a"	"1"	"1"	"1"	"1"	"1"
"both"	"q"	"w"	"b"	"b"	"2"	"BB"	"another descrp"	"11"	"12"	"1"	"s1b"	"s2b"	"1"	"1"	"1"	"1"	"1"
"1"	"q"	"w"	"c"	"c"	"5"	"CC"	"despript A"	"12"	"13"	"1"	"s1c"	"s2c"	"1"	"1"	"1"	"1"	"1"
"2"	""	""	""	""	"4"	"DD"	"some more stuff"	"14"	"14"	"4"	"s1d"	"s2d"	""	""	""	""	""