Now that you've provided an indication of your data,
a much better solution (than my earlier tentative suggestion) presents itself.
Assuming you have a filehandle, e.g. $matches_fh,
to your file of match data (Genomes_used_Hant.txt in your example);
and another, e.g. $fasta_fh, to your fasta data (NRT2.txt in your example);
you can capture the wanted counts like this:
my $alt = join '|', reverse sort <$matches_fh>;
my $re = qr{(?x: ^ > ( $alt ) )};
my %count;
/$re/ && ++$count{$1} while <$fasta_fh>;
The code you've presented, in a couple of your posts in this thread,
use the 3-argument form of open with lexical filehandles:
this is very good.
You are not, however, checking for I/O errors: this is not good at all.
The easiest method is to let Perl do this checking for you
with the autodie pragma;
the alternative is to do this yourself,
as shown in the open documentation.
In the test code below, I've used Inline::Files
purely for convenience.
The count information is in %count: you can format and output this however you want.
#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dump;
use Inline::Files;
my $alt = join '|', reverse sort <MATCHES>;
my $re = qr{(?x: ^ > ( $alt ) )};
my %count;
/$re/ && ++$count{$1} while <FASTA>;
dd \%count;
__MATCHES__
Gloin1
XYZ1
XYZ
XYZ12
__FASTA__
>Gloin1_1
unwanted data
>XYZ_1
unwanted data
>XYZ12_1
unwanted data
>XYZ1_2
unwanted data
>XYZ1_1
unwanted data
>XYZ12_3
unwanted data
>Gloin1_2
unwanted data
>XYZ12_2
unwanted data
Output:
{ Gloin1 => 2, XYZ => 1, XYZ1 => 2, XYZ12 => 3 }
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