[BioPython] PSI-Blast

[Naveed Iqbal]

Hello,
      Has anyone had any experience/success in running PSI-Blast
locally? I used the code from the tutorial and it doesn't seem to work.
I am running it on windows. I have the latest update of BioPython
(1.10).
Here is the code I have been trying to run.
Any comments?
------------------------------------------------
from Bio.Blast import *
from sys import *
file = "E:\\python22\\test.fa"
blastexe = 'E:\\blast\\blastpgp.exe'
database='E:\\blast\\prot'

E_VALUE_THRESH = 0.04

blast_out, error_info = NCBIStandalone.blastpgp(blastexe,database,file)

b_parser = NCBIStandalone.PSIBlastParser()
print "done"
# this creates a Bio.Blast.Record.PSIBlast
b_record = b_parser.parse(blast_out)
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Here is the error I get.

  r, w, e = popen2.popen3([blastcmd] + params)
  File "E:\Python22\lib\popen2.py", line 130, in popen3
    w, r, e = os.popen3(cmd, mode, bufsize)
TypeError: popen3() argument 1 must be string, not list
------------------------------------------------------
Any help would be appreciated


Naveed Iqbal