[pygr-notify] Issue 79 in pygr: Multi-sequence blast support

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Comment #3 on issue 79 by alexander.alekseyenko: Multi-sequence blast  
support
http://code.google.com/p/pygr/issues/detail?id=79

Code:

import blast,seqdb

seqDB = seqdb.BlastDB('1.TCA.454Reads.fna')
refDB = seqdb.BlastDB('pNL43.may13.fasta')

blastMap = blast.BlastMapping(refDB)

z=blastMap(None,al=None,queryDB=seqDB)

Where 1.TCA.454Reads.fna has LOTS of sequences and pNL43.may13.fasta has  
only one.

Full error:

Exception in thread Thread-1:
Traceback (most recent call last):
   File
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/threading.py",  
line
460, in __bootstrap
     self.run()
   File
"/Users/alexander/inc/pygr_test/pygr/build/lib.macosx-10.5-i386-2.5/pygr/blast.py",
line 56, in run
     for seqID, seq in self.seqDB.iteritems():
   File "seqdb.py", line 299, in iteritems
     yield seqID, self[seqID]
   File "seqdb.py", line 314, in __getitem__
     self._weakValueDict[seqID] = s # save in cache.
   File "classutil.py", line 392, in __setitem__
     self.keep_this(v)
   File "classutil.py", line 389, in keep_this
     del self._keepDict[vmin]
KeyError: 004294_0715_3536[0:94]

The exact sequence where the error occurs differs from run to run.

blast_test.py doesn't run with a strange error:
$ python blast_test.py
unable to import extension module: cannot import name cnestedlist

I presume that the main difference between blast_test.py and my test is  
that my
queryDB has many more sequences than the test.





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