[Biopython] Problems parsing with PSIBlastParser

[Michiel de Hoon]

> Did you get any reply?
> 
Yes, but just that they'll look into it. Nothing concrete yet, but I guess changing the Blast XML output is something that needs to be done very carefully, so it may take a while. Will keep you guys posted if I get a reply.

--Michiel.

--- On Tue, 11/3/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] Problems parsing with PSIBlastParser
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Cc: "Biopython Mailing List" <biopython at lists.open-bio.org>
> Date: Tuesday, November 3, 2009, 7:52 AM
> On Fri, Oct 16, 2009 at 1:04 AM,
> Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
> >
> > Last time I checked (which was a few weeks ago), a
> multiple-query PSIBlast
> > search gives a file consisting of concatenated XML
> files. The problem is in
> > the design of Blast XML output. For a single-query
> PSIBlast, the fields under
> > <BlastOutput_iterations> are used to store the
> output of the PSIBlast iterations.
> > For multiple-query regular Blast, the same fields are
> used to store the search
> > results of each query. With multiple-query PSIBlast,
> there is then no way to
> > store the output in the current XML format. I've been
> meaning to write to NCBI
> > about this, but I haven't gotten round to it yet. Will
> do so this weekend.
> >
> > --Michiel.
> 
> Did you get any reply?
> 
> Peter
>