[BioPython] qblast

[Michael S. Robeson]

>
> 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

Okay will do!

> 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.

Actually I have another script which actually parses the blast and  
genbank data but this was one of the first scripts I wrote to make  
sure I can to the 'simple' things first. But I essectially use the  
same code to run blast.
>
> 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).

Yes it is. I must have thought I changed those parameters when in  
fact I didn't. Thanks for checking on this!

> > 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 Can you point out any out of date documentation please?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

Okay, I must have been looking in the wrong places then. I'll go  
through the listed tutorials again. Is there a particular one you'd  
suggest? I have only looked at a few of the 'Online course notes'  
which is probably why. I just noticed the tutorial cookbook links. I  
must be blind!

And I am using the latest biopython (1.43) package as installed via  
fink for OS X.

Again, thanks! I'll play around with this more over the next day or  
so. I'll see if I can get my code to switch settings and see how the  
results are affected.

-Mike