[Biopython] Legacy blastn XML outfile parsing is slow. What XML parser is actually used?

[Michiel de Hoon]

> The same goes with the attribute names. I suppose I
> could add one table in the draft tutorial to list the
> new attribute names, but I prefer not to have any
> Bio.Blast-compatible names in the code.

>> I would have to lookup how the record attributes
>> changed(=renamed) from those specific for blast to
>> those generalized and used(=promoted)
>> by SearchIO.

>> I see, hsp.sbjct_start is renamed to hsp.hit_start ...

I would suggest to use the same names as in the XML source file. Then we are consistent with NCBI, we don't have to come up with our own names, and we won't have to provide a list of biopython-defined record attributes. Dropping the "Hsp" in <Hsp_hit-from>, that would be "hit-from".

Best,
-Michiel.