[Bioperl-l] Bio::DB::Fasta and threads

[Fields, Christopher J]

On Dec 3, 2012, at 6:29 PM, Leon Timmermans <l.m.timmermans at students.uu.nl> wrote:

> On Mon, Dec 3, 2012 at 3:36 AM, Florent Angly <florent.angly at gmail.com> wrote:
>> The first issue is the serialization of Bio::DB::IndexedBase-inheriting
>> (e.g. Bio::DB::Fasta and Bio::DB::Qual) objects, which is needed for
>> threading (for example when using Thread::Queue::Any). I implemented hooks
>> that make it transparent to serialize using Storable freeze() and thaw().
> 
> I don't think serializing a magical thingie makes much sense. Storable
> is commonly used for a lot more things than interthread communication
> (e.g. network communication), this would often not work under such
> circumstances.
> 
> Leon

Leon, any suggestions on alternatives?  I know this particular bit is a sore spot with MAKER at the moment, so any help would be greatly appreciated.

chris