[Biopython] Problems parsing with PSIBlastParser

[Peter]

You don't have to include *all* the previous email in the quote ;)

On Thu, Oct 15, 2009 at 4:33 PM, Miguel Ortiz Lombardia
<ibdeno at gmail.com> wrote:
>>>
>>> I suspect they will tell us to use the XML output, but then, not all
>>> info I need seems to go there...
>>
>> i think the same, and i suspect the XML output doesn't suffer of the
>> same problem.
>
> For me the XML is a no issue, since the NCBIXML parser does not really
> support PSI-BLAST searches:
> it can't get information on the rounds, convergence... If you have a look to
> NCBIXML.py you see a lot of XXX TODO PSI...

There may well be some things missing in our parser, but last time I checked,
the XML file itself was missing lots of information found in the plain
text output.

Peter