Bio::SeqFeature speedup using caching and cloned instances

location speedup

cjfields@pyrimidine:~/tests/seq$ cat locations_bm.pl 
#!/usr/bin/perl -w

use Modern::Perl;
use Bio::SeqIO;
use Benchmark qw(cmpthese);

my $file = shift;

cmpthese(10, {
        'default' => \&default_location,
        'cached' => \&cached
    });

my $ct1 = my $ct2 = 0;

sub default_location {
    my $in = Bio::SeqIO->new(-file => $file,
                             -format  => 'genbank');
    
    while (my $seq = $in->next_seq) {
        for my $sf ($seq->get_SeqFeatures) {
            next unless $sf->primary_tag eq 'CDS';
        }
    }
}

sub cached {
    my $in = Bio::SeqIO->new(-file => $file,
                             -format  => 'genbank');
    $in->location_factory->cache(1);
    while (my $seq = $in->next_seq) {
        for my $sf ($seq->get_SeqFeatures) {
            next unless $sf->primary_tag eq 'CDS';
        }
    }
}
cjfields@pyrimidine:~/tests/seq$ perl locations_bm.pl NC_014922.txt
        s/iter default  cached
default   2.08      --    -26%
cached    1.54     35%      --
cjfields@pyrimidine:~/tests/seq$