[BioPython] empty xml after local blast
Stefanie Lück
lueck at ipk-gatersleben.de
Tue Jan 8 14:18:08 UTC 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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