Thanks for a great reply. This was exactly what I was looking for.

It is quite time consuming to do the indexing, currently is taken > 2 hours (still running), but the lookups seem much faster. Testing it out on a smaller dataset, there is a 3x time reduction vs grep, and I'll have to see how that scales with the full dataset.

I did some modifications to the code, adapting it to the Lucy::Simple module, so right now it looks like this:

#!/usr/bin/perl
use 5.014;
use strictures;
use Lucy::Simple;

my $index = $ARGV[0];
system("mkdir -p $index");
my $lucy = Lucy::Simple->new(
    path     => $index,
    language => 'en',
);

open DATA, '<',$ARGV[1];
while (my $line = <DATA>) {
    my ($id,$taxid,$text) = split(/;/, $line, 3);
    $lucy->add_doc( {id => $id, content => $text} );
}
[download]

#!/usr/bin/perl
use 5.014;
use strictures;
use Lucy::Simple;

my $index = Lucy::Simple->new(
    path     => $ARGV[0],
    language => 'en',
);

my $query_string = $ARGV[1];
my $total_hits = $index->search(query => $query_string);

#print "Total hits: $total_hits\n";
while ( my $hit = $index->next ) {
    print "$hit->{id}\t";
    print "$hit->{content}";
}
[download]