[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:

print error_info.read()

or:

save_file =open("blast.error","w")
blast_result=error_info.read()
save_file.write(blast_result)
save_file.close()

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 :)

Peter



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