#!/usr/bin/perl
use strict;
use warnings;

my $count;
while (<>) {
    if ($_ =~ /^>hsa/){
	chomp (my $line = <>);
	$count .= length($line);
        $count .= " ";
	print "Count final: " . $count . "\n";
    }
} continue {
    close ARGV if eof; # reset $. each file
}

my $filename = 'counts.txt';

open (my $fh, '>', $filename)
    or die "Could not open '$filename' $!";

print $fh $count;

close $fh
    or die "Could not close '$filename' $!";

__END__

$ perl test.pl test.txt
Count final: 107
Count final: 107 251