[BioPython] qblast + documentation

[Peter]

Michael S. Robeson wrote:
>>> 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 Can you point out any out of date documentation please?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?

The main tutorial is probably best, and most up to date.
http://biopython.org/DIST/docs/tutorial/Tutorial.html

If you are interested in RPS-BLAST, then have a look here too:
http://www.warwick.ac.uk/go/peter_cock/python/rpsblast/

 > 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!

There have been changes in how we handle parsing Blast output in recent 
releases of Biopython (driven by changes the NCBI made).  We are are now 
recommending the use of XML output, but the Biopython code used to do 
this had to change a little compared to older releases.

This may mean that any "third party" tutorials are a little out of date now.

Peter