#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
use feature 'say';

my %hash;
# reset line numbering on each input file
while (<>) {
    chomp;
    next if /^\s*$/; # skip blank lines
    say "$.\t$_";
    $hash{$ARGV}{$.} = $_;
} continue {
    close ARGV if eof;  # Not eof()!
}

print Dumper \%hash;

__END__

$ perl test.pl file1.txt file2.txt
1	ABS0056
3	ABS0057
5	ABS0058
7	ABS0059
1	ABS0060
3	ABS0061
5	ABS0062
7	ABS0036
$VAR1 = {
          'file2.txt' => {
                           '7' => 'ABS0036',
                           '5' => 'ABS0062',
                           '1' => 'ABS0060',
                           '3' => 'ABS0061'
                         },
          'file1.txt' => {
                           '5' => 'ABS0058',
                           '7' => 'ABS0059',
                           '1' => 'ABS0056',
                           '3' => 'ABS0057'
                         }
        };