Hi Alex, I implemented your multi-sequence blast feature on pygr.blast.BlastMapping. All you have to do is pass a queryDB argument (which should be a dictionary of sequences with IDs, just as you did it in your code) when you call the BlastMapping object (i.e. the BlastMapping interface is simply that you use the object as a callable and get back the alignment object as the return value). Take a look at pygr/tests/blast_test.py's test_multiblast() for an example of how to do this. Get the latest code from the master branch of the public git repository (repo.or.cz).
Currently, this feature is only available for BlastMapping (which handles blastn, blastp, and tblastn), but not yet for MegablastMapping or BlastxMapping (which handles blastx and tblastx). BlastDB is deprecated; use the BlastMapping pattern instead. No more features for 0.8... -- Chris On Mar 18, 2009, at 11:21 AM, Alexander Alekseyenko wrote: > > 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? > > Cheers, > Alex --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
