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

[Stefanie Lück]

Thanks Peter!

C:\Blast\blastall.exe worked!.
Sorry for the drive mistake, I have it on both...

But my xml File is empty :-(
I'll try to fix it...

standalone blast version is blast-2.2.17-ia32-win32.exe

Stefanie


----- Original Message ----- 
From: "Peter" <biopython at maubp.freeserve.co.uk>
To: "Stefanie Lück" <lueck at ipk-gatersleben.de>
Cc: <biopython at lists.open-bio.org>
Sent: Tuesday, January 08, 2008 11:46 AM
Subject: Re: [BioPython] blastall does not exist at %s" % blastcmd


On Jan 8, 2008 9:06 AM, Stefanie Lück <lueck at ipk-gatersleben.de> wrote:
> 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)
> ...
> blastall.exe is in this folder (checked by os.listdir()) but can't be 
> found from the tool.
>

Could you try this, which is the test done in the Biopython blastall
function that triggers the error message you saw:

print os.path.exists(my_blast_exe)

Could you also double check the path is C:\Blast\bin\blastall.exe and
not perhaps C:\Blast\blastall.exe (the NCBI changed this at some point
on Windows). Also did you install it to the F: drive where your
database is, rather than C: ?

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

What version of standalone blast do you have?

Peter