[pygr-notify] Issue 49 in pygr: Initial delay for membership checking in seqdb.BlastDB

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Updates:
	Status: WontFix
	Cc: ti... at idyll.org
	Labels: -Priority-Critical Priority-Low Milestone-Release0.8

Comment #1 on issue 49 by cjlee112: Initial delay for membership checking  
in seqdb.BlastDB
http://code.google.com/p/pygr/issues/detail?id=49

BlastDB is deprecated.  Use SequenceFileDB instead as the standard sequence  
database
class.

The delay that Namshin reported is due to BlastDB's support for NCBI ID  
mangling
(i.e. the fact that NCBI blastall reports back "fake ID"s that do not match  
the
original ID in the FASTA file.  BlastDB handles this by creating a lookup  
table for
translating the fake IDs to the correct IDs.  The first request for an ID  
that
doesn't match triggers construction of this table, thus the delay.  Note  
also that
construction of this table will take up memory as well.

The solution is simple: switch to using the base class (SequenceFileDB, or
BlastDBbase which adds blast() etc. methods) unless you really need the  
NCBI ID
mangling support -- in which case this delay is unavoidable.

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