[Biopython] Problems parsing with PSIBlastParser

[Peter]

On Wed, Oct 14, 2009 at 12:30 PM, Miguel Ortiz Lombardia
<miguel.ortiz-lombardia at afmb.univ-mrs.fr> wrote:
>
> Hi again, Peter.
>
> Well, it turned out that I don't have such work-around... When I launched
> the script as:
>
> nohup lpbl.py ... &
>
> against all my sequences it choked at the first one (quite longer than the
> one I was using as an example) with the very same error.

It would take longer as it would wait for BLAST to finish before starting
to parse it.

> However, this time I have the "temp.txt" file and indeed there lines such as:
>
> Query: 0    -
>
> Sbjct: 445  G                                                            445
>
> Query: 0
>
> Sbjct: 445  G                                                            445
>
> Query: 0    ------
>
> Sbjct: 1316 ETNAPV
> 1321
>
> present for some alignments and it cannot be parsed by my code.

Those do look strange.

> When I run blastpgp myself on the command line, same arguments, and catch
> the standard output to a temp2.txt file, the latter file does not contain
> those lines and can be parsed correctly.

This is odd, and I am not sure what would cause this.

> So, in the end I went back to my code and modified according to your
> recommendation of using the commandline applications. The relevant part of
> code now looks like this:
> ...
> And it works!

Great - I'm glad my vague instructions made sense :)

> Thanks again for your help,

At least we have solution, even if we didn't get to the bottom of
the strange BLAST output. I'll close the bug...

Peter