[BioPython] [Bug 2502] PSIBlastParser fails with blastpgp 2.2.18 though works with blastpgp 2.2.15

[Peter]

On Wed, May 21, 2008 at 2:53 PM, Miguel Ortiz-Lombardía
<ibdeno at gmail.com> wrote:
> Peter, I'm sending this to you because bugzilla rejected my e-mail:

I don't think you can submit comments to the bugs on bugzilla via
email.  You have to go to our bugzilla webpage (using the link
included in the email) and fill in the comments box.  i.e.
http://bugzilla.open-bio.org/show_bug.cgi?id=2502

> Hi,
>
> Just to clarify: the output is not XML but plain text ( because
> align_view='0' ) Is the plain text that you want?

I had forgotten to check what the default output was - sorry.

To cover all cases, I would like to see both the plain text and the
XML for both the old and new blast versions.  i.e. Four different
files using the same input query and database.  I would generate these
on the command line.

It may we that its only a simple change to the plain text (but I
suspect not), and that updating the plain text parser would be simple.

I fear that the changes to the plain text are bigger (based on what
happened with the other blast tools recently) and we would be better
off getting Biopython to parse the XML.

Thanks,

Peter