[BioPython] qblast

[Peter]

Michael S. Robeson wrote:
> Sure, I am using a really simple script that I wrote (link below) to  
> start getting familiar w/ biopython. So, any other comments would be  
> greatly appreciated.
 >
 > http://ucsu.colorado.edu/~robeson/documents/blast.txt

Assuming you are using Biopython 1.43, then I would have suggested using 
Bio.SeqIO rather than Bio.Fasta for reading/writing FASTA files. See the 
tutorial or http://www.biopython.org/wiki/SeqIO

I'm also unclear why you want to save individual output blast HTML pages 
(one file per sequence). Trying to parse these HTML files later will be 
a pain - go from the XML output if you want to read the blast output 
with Biopython.

> I assumed the above was the same as biopython's default qblast when  
> using blastn. Basically, my script seemed worked fine until NCBI  
> changed the layout of their site (I'd check every so often with a set  
> of samples).

See my other email - they should be the same if all the parameters are 
the same (specifically it looks like the NCBI seems to be using 
different defaults for the gap penalties, which was very confusing).

 > I also tried to change my code with some of the new
> biopython code. But it is very hard to find good up-to-date  
> tutorials. Last time I looked none of them worked.

Can you point out any out of date documentation please?
As far as I know, the BLAST examples in our tutorial work fine:
http://biopython.org/DIST/docs/tutorial/Tutorial.html

Peter