[pygr-notify] Issue 44 in pygr: tblastn and blastx support

[codesite-noreply at google.com]

Updates:
	Status: Fixed

Comment #4 on issue 44 by cjlee112: tblastn and blastx support
http://code.google.com/p/pygr/issues/detail?id=44

implemented BlastxMapping and BlastxResults classes as well as
generate_tblastn_ivals() generator function.

Here's a simple example of blastx usage:

from pygr import seqdb, blast
dna = seqdb.SequenceFileDB('hbb1_mouse.fa')
prot = seqdb.SequenceFileDB('sp_hbb1')
blastmap = blast.BlastxMapping(prot)
results = blastmap[dna['gi|171854975|dbj|AB364477.1|']]
for result in results:
     for src,dest,edge in result.edges():
         print '%s %s\n%s %s\n' %(src,repr(src),dest,repr(dest))

BlastMapping will raise a ValueError if you try to use it for blastx;  
BlastxMapping
will raise a ValueError if you try to use it for anything other than blastx  
or tblastx.



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