[BioPython] Blast XML parser
Christof Winter
winter at biotec.tu-dresden.de
Wed Dec 13 10:40:26 UTC 2006
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.
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