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

my $filename = 'counts.txt';

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

chomp(my @lines = <>);

for (@lines) {
    next if ($_ =~ /^>hsa/);
    print $fh length($_) . " ";
}

print $fh "\n";

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

__END__

$ cat counts.txt
107 251