[BioPython] PSIBlastParser and blastpgp 2.2.18

[Peter]

On Wed, May 21, 2008 at 8:43 AM, Miguel Ortiz-Lombardía
<ibdeno at gmail.com> wrote:
> Hi,
>
> The PSIBlastParser (biopython 1.45) seems not to work with the latest
> (2.2.18) version of NCBI blastpgp. Using the same script/inputs I can
> successfully run it with blastpgp 2.2.15 but when using 2.2.18 I get this
> error:
>
> Traceback (most recent call last):
> ...
> ValueError: Invalid header?
>
> In both cases I had setup align_view='0' so the psi-blast output is plain
> text and not XML (This is because I don't think there is a PSI-Blast parser
> working with XML, if there is one, please let me know how to invoke it)

Plain text Blast parsing in general is a pain as the NCBI often make
minor changes to the file format.  If you could file a bug on
Bugzilla, with a couple of example input files, I'll try and have a
look and see if its an easy fix this time.  Matched pairs using
blastpgp 2.2.15 and 2.2.18 with the same command line arguments would
be especially useful.

In the meantime, you could try the Bio.NCBIXML parser on the PSI-Blast
XML output.  I know that works for blastall and rpsblast, so it may be
OK with blastpgp too.  Please let us know if this works for you (and
we can update our documentation).

Thank you,

Peter