[Biojava-dev] Fwd: [blast-announce] New Version of BLAST XML output

[Peter Cock]

On Wed, May 6, 2015 at 6:02 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>On Tue, May 5, 2015 at 1:18 PM, Paolo Pavan <paolo.pavan at gmail.com> wrote:
>>
>> As seen in other Bio projects, aside with Sequence IO and Alignment IO
>> procedures it could have a Search result IO also.
>
> I never understood why other Bio* projects have special Blast modules.
> Perhaps XML parsing is not as easy as it is in Java? Please see the code at
> the bottom of this message.

Python at least has a range of XML parsing libraries which are up to the
task. However, as Paolo wrote:

>> The advantage is to define common data structures that models Hsp, Hits,
>> Results without taking care (ie. making abstraction) of the underlying
>> search program.

This is the big advantage of BioPerl and Biopython's SearchIO module.
You can at least in theory switch between parsing BLAST XML, BLAST
tabular, BLAST plain text (shudder), or another related format without
major changes to your code.

> and the disadvantage is that you constantly need to update them to the
> variant of blast plus version of the output file format.

I think it is much better to have this housekeeping done once centrally in
a Bio* library that re-invented by anyone parsing the BLAST output.
However, the NCBI BLAST XML output has been fairly stable, and the
new output has a formal schema so should be even more dependable.

Peter