fragment id  index 
accb     10  A
bbc      11  B
ccd      12  C 

##</code><code>##

fragment id index
ccd      15   D     
llk      11   B
kks      12   C

##</code><code>##

fragment  id_file file 1   id_file2      file 2
accb         10      1                    0
bbc          11      1       14           1
ccd          12      1       15           1   
llk                  0       11           1
kks                  0       12           1

##</code><code>##

use strict;
use warnings;
use feature qw(say);
use autodie;
use Text::CSV_XS;

use constant {
    FILE_1  => "1.csv",
    FILE_2  => "2.csv",
 
};
 
my %hash;
#
# Load the Hash with value from File #1
#
open my $file1_fh, "<", FILE_1;
while ( my $value = <$file1_fh> ) {
    chomp $value;
    $hash{$value}++;
}
close $file1_fh;
#
# Add File #2 to the Hash
#
open my $file2_fh, "<", FILE_2;
while ( my $value = <$file2_fh> ) {
    chomp $value;
    $hash{$value} += 10;   # if the key already exists, the value will now be 11
                           # if it did not exist, the value will be 10
}
close $file2_fh;

open my $file3_fh, "<", FILE_3;
while ( my $value = <$file3_fh> ) {
    chomp $value;
    $hash{$value} += 100;
}
close $file3_fh;

for my $k ( sort keys %hash ) 
{   if ($hash{$k} == 1) { # only in file 1
        say "$k\t1\t0";
    }
    elsif ($hash{$k} == 10) { # only in file 2
        say "$k\t0\t1";
    }

    else { # in both file 1 and file 2
        say "$k\t1\t1";
    }
}

open (OUT, ">final.csv") or die "Cannot open OUT for writing \n";
$, = " \n";
print OUT "fragment\tid_file\tfile1\tid_file2\tfile2\n\n";

print OUT (sort keys %hash);
close OUT;