Hope it's not too late for this release, but I have one comment. BlastDB method blast can only process one sequence at a time, which can be slow due to numerous system calls when blasting a large database against some other database. I have uploaded to this group my implementation of processing a whole database in just one invocation of .blast method (see roche454.tgz:roche.py: blast_processor, process_library_blast and ReferenceDB.blast_library). The implementation creates a blast process in a thread that listens to fasta sequences being piped into it, feeds them into blast and writes blast results into return pipe. Do you think this can be included in the release?
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