[BioPython] Need help on NCBIStandaloneblast
Peter (BioPython List)
biopython at maubp.freeserve.co.uk
Thu Mar 30 10:56:29 EST 2006
Halima Rabiu wrote:
> Hi everyboby ;
> I am new to biopython having problems with the "NCBIStandalone.blastall".
> After launching the Blast with "doBlast" it look like runs and end
> and then I check the output it empty and I try same thing using comand
> line it work and get result.
> I attch my code.
Have you checked the paths are correct, e.g.
assert os.path.isfile(data), "Missing database file " + data
assert os.path.isfile(infile), "Missing input file " + infile
You don't need to check blast_exe yourself, as the blastall command does
this for you.
If I understood you correctly, the "blast.out" file is empty.
Did blast return any error message? Try:
Next question, could you tell us what you typed at the command line
which does work?
> I also try to go though the previous posts on biopython mailing list fund
> similar problem post by Andreas but no solution to the problem .
It was worth checking anyway :)
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