[BioPython] Blast XML parser

[Christof Winter]

Dear Michiel:

Michiel de Hoon wrote:
> Thanks, Christof.
> 
> Christof Winter wrote:
>> The result looks fine, however, it seems that query IDs and 
>> definitions are not parsed. This is probably because of NCBI's change 
>> of tag names from
>  > ...
> You're right. I've fixed this in an updated patch (at bug #1970 on 
> Bugzilla).

Works fine! Thanks a lot for this, Michiel.

>> Concerning the new syntax, I would prefer a unified syntax for parsing 
>> of both XML formats, and I would like to vote for Peter's "nice idea" 
>> in his comment #6 in 
>> http://bugzilla.open-bio.org/show_bug.cgi?id=1970). Running the same 
>> code on different machines with different local BLAST versions 
>> constantly gives me a headache when parsing the results. As long as 
>> these different BLAST versions are out there, people will run into 
>> problems, and fill the BioPython discussion lists.
> 
> I'm not sure if I understand correctly. Are you saying that we should 
> have one function to handle both old- and new-style XML output? Or are 
> you referring to how the functions should be named?

What I meant is: I would prefer that the same BioPython code is able to parse any NCBI 
Blast XML output format.
That is, we should have one function for both old- and new-style XML output. The actual 
naming of functions is not so important for me, I also wouldn't mind having a new naming 
or syntax, as long as it can be used for either format. Personally, I favour iterators, 
since they are simple and elegant.

Cheers,
Christof

> 
> --Michiel.