[BioPython] Problems runing BLAST

Bruno Santos bsantos at biocant.pt
Wed Jan 23 12:55:18 EST 2008


Hi
I use to run blastall without any problems, but now I have moved all my scripts to a server runing Fedora Core 6 and now I get the folowing error when parsing the blast results:

Traceback (most recent call last):
  File "/usr/local/lib/python2.5/site-packages/Bio/Blast/NCBIXML.py", line 568, in parse
    raise SyntaxError("Your XML file did not start <?xml...")
SyntaxError: Your XML file did not start <?xml...

I'm runing blastall version 2.2.16. 
And my code looks like this:
my_blast_file = "file.fasta"
my_blast_exe = "/usr/local/bin/blastall"
result_handle, error_info = NCBIStandalone.blastall(my_blast_exe, "blastn",my_blast_db, my_blast_file, expectation)  
blast_records = NCBIXML.parse(result_handle)


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