[BioPython] blastall does not exist at %s" % blastcmd

Stefanie Lück lueck at ipk-gatersleben.de
Tue Jan 8 09:06:40 UTC 2008


Hi!

I'm trying to get a local blast running. I proceeded as described in the cookbook but I allways get this Error message:
>>>
Traceback (most recent call last):
  File "F:\Blast\blast.py", line 10, in <module>
    my_blast_db, my_blast_file)
  File "C:\Python25\Lib\site-packages\Bio\Blast\NCBIStandalone.py", line 1499, in blastall
    raise ValueError, "blastall does not exist at %s" % blastcmd
ValueError: blastall does not exist at C:\Blast\bin\blastall.exe
<<<

>>>
My Code:

import Bio
from Bio.Blast import NCBIStandalone
import os

my_blast_db = r"F:\Blast\primerdb"
my_blast_file = "test.fasta"
my_blast_exe = r"C:\Blast\bin\blastall.exe"

result_handle, error_info = NCBIStandalone.blastall(my_blast_exe, "blastn",
my_blast_db, my_blast_file)
blast_results = result_handle.read()
save_file = open("my_blast.xml", "w")
save_file.write(blast_results)
save_file.close()
<<<

blastall.exe is in this folder (checked by os.listdir()) but can't be found from the tool.

I'm using Python 2.5 and biopython-1.44.win32-py2.5.exe.

Does somewone has idea where's the problem?

Greetings 
Stefanie



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