[BioPython] empty xml after local blast

Stefanie Lück lueck at ipk-gatersleben.de
Tue Jan 8 09:18:08 EST 2008


Hi again!

I got blastall running but my xml output file is empty...
Any ideas? 
Where exactly must be my fasta file?

>>>
Code:
import Bio
from Bio.Blast import NCBIStandalone
import os

my_blast_db = r"C:\Blast\primerdb"
my_blast_file = "test.fasta"
my_blast_exe = r"C:\Blast\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()
>>>

I'm using Python 2.5, biopython-1.44.win32-py2.5.exe and blast-2.2.17-ia32-win32.exe

Regards 
Stefanie


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