[BioRuby] Blast with file as a query option?

[Kevin English]

Hello,
  I have to very large local fasta files that wish to blast against one
another and parse the results in bio ruby. I'm wondering if there is a way
to mimic the behavior of this blast command:

blastall -p blastn -i Large_list_sequences_1.fasta -d Large_list_sequences_2


where Large_list_sequences_2 is a formatted fasta db. My current
implementation opens Large_list_sequences_1.fasta and goes through it
sequence by sequence. It seems to run pretty slow. I'm wondering if I can in
some way do the above blast command and loop through the results and get a
performance gain.

For any curious, my code is on github:

http://github.com/kenglishhi/bioflexrails/tree/master

The file that is doing the blasts is under app/model/biodatabase.rb.

I'm trying to write a rails app uses biosql db and allows this biologist to
organize his sequences. I'm very new to bioinformatics but have a lot
experience with Ruby on Rails.

Thanks in advance for you help.

Kevin