[BioPython] Need help on NCBIStandaloneblast

[Halima Rabiu]

Thanks Peter , I have been able to trace the error when I print the 
error_info.read() 
the error is with my infile 
There is result in my save file now but I am still having problem passing 
the output file.But I will try to figure it out it may be syntax problem
Thanks

On Thu, 30 Mar 2006, Peter (BioPython List) wrote:

> 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
> 
>