#!perl
use strict;
use warnings;
use List::MoreUtils 'uniq';
use Text::CSV_XS;

my %files = (file1 => '1.csv', file2 => '2.csv');
my %hashes;
my $csv   = Text::CSV_XS->new( { binary => 1 } );

for my $file (keys %files)
{
    open(my $in, '<', $files{$file})
        or die "Cannot open file '$files{$file}' for reading: $!";

    <$in>;      # Discard column headings

    while (my $row = $csv->getline($in))
    {
        my $key = shift @$row;
        $hashes{$file}{$key} = [ @$row ];
    }

    close $in
        or die "Cannot close file '$files{$file}': $!";
}

separator_line();
print join("\t", qw(frag id1 file1 id2 file2)), "\n";
separator_line();

my   @keys;
push @keys, keys %$_ for values %hashes;
     @keys = uniq @keys;

for my $fragment (sort @keys)
{
    my $f1 = exists $hashes{file1}{$fragment} ? 1 : 0;
    my $f2 = exists $hashes{file2}{$fragment} ? 1 : 0;

    printf "%s\t%s\t%s\t%s\t%s\n",
            $fragment,
            $f1 ? $hashes{file1}{$fragment}->[0] : '',
            $f1,
            $f2 ? $hashes{file2}{$fragment}->[0] : '',
            $f2,
}

separator_line();

sub separator_line
{
    print '-' x 37, "\n";
}