#!/usr/bin/env perl 
use strict;
use warnings;
use Test::More;
use File::Slurp;
#Counter.pl

open my $handle, '<', "/home/nic/Desktop/5-27-17/Genomes_used_HANT.txt
+";
chomp(my @HANT = <$handle>);
close $handle;


my @counts = (0,1,2,3,4,5,6,7,8,9,10);
plan tests => scalar @hant;

my $nrt2 = read_file("/home/nic/Desktop/5-27-17/NRT2.txt");

for my $hant (@HANT) {
    my $matches = () = my $nrt2 =~ /$hant/g;
    is ($matches, shift @counts, "Number of matches found for $hant");
}
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This:

chomp(my @HANT = <$handle>);
...
plan tests => scalar @hant;
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Perl is case sensitive, unless otherwise stated for details. @HANT and @hant are different arrays.

perl -le'print map{pack c,($-++?1:13)+ord}split//,ESEL'

#!/usr/bin/env perl 
use strict;
use warnings;
use Test::More;
use File::Slurp;
#Counter.pl

open my $handle, '<', "/home/nic/Desktop/5-27-17/Genomes_used_HANT.txt
+";
chomp(my @HANT = <$handle>);
close $handle;

my @counts = (0,1,2,3,4,5,6,7,8,9,10);
plan tests => scalar @HANT;

my $nrt2 = read_file("/home/nic/Desktop/5-27-17/NRT2.txt");

for my $hant (@HANT) {
    my $matches = () = $nrt2 =~ /$hant/g;
    is ($matches, shift @counts, "Number of matches found for $hant");
}
[download]

Ok this works now and correctly returns count. The only problem is that it returns errors and extra junk as well. How do I get rid of it? Why does it show expected values?

nic@nic-VirtualBox:~/Desktop/5-27-17$ perl Counter.pl
1..612
ok 1 - Number of matches found for Laesu1
ok 2 - Number of matches found for Patat1
not ok 3 - Number of matches found for Hydru2
#   Failed test 'Number of matches found for Hydru2'
#   at Counter.pl line 18.
#          got: '1'
#     expected: '2'
not ok 4 - Number of matches found for Armost1
#   Failed test 'Number of matches found for Armost1'
#   at Counter.pl line 18.
#          got: '0'
#     expected: '3'
not ok 5 - Number of matches found for Pacta12
#   Failed test 'Number of matches found for Pacta12'
#   at Counter.pl line 18.
#          got: '1'
#     expected: '4'
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I just want this for example.

Number of matches found for Pacta12: 1 

Number of matches found for Armost1: 0
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