[BioPython] empty xml after local blast

[Stefanie Lück]

Thanks, it's couldn't find the database!
Great help, thanks a lot ;-)

----- 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 3:33 PM
Subject: Re: [BioPython] empty xml after local blast


On Jan 8, 2008 2:18 PM, Stefanie Lück <lueck at ipk-gatersleben.de> wrote:
> Hi again!
>
> I got blastall running but my xml output file is empty...
> Any ideas?

Have you ever tried running blastall.exe from the command line "by
hand"?  This can be very useful, and would let you rule out several
basic problems (e.g. make sure blast is installed correctly, and that
your database is working).

> Where exactly must be my fasta file?

Where ever you like - as long as you specify its location correctly.
Your code below seems to assume that "test.fasta" is in the current
directory (i.e. where you are running your python script from).  Is
this correct?

It may be simpler to use a full path, e.g.
my_blast_file = r"C:\temp\test.fasta"

I suspect that Standalone blast is not finding the input file, or that
it is not finding your database.  If you get an empty XML file, one
thing to try is checking the error output from the command line call:

print error_info.read()

Peter