[Bioperl-l] parsing psiblast report...

[Peter Schattner]

Geetha Vasudevan wrote:

> I am trying to parse psiblast reports for the HSPs of the query and the
> subject sequences. The blast ouptut contains more than one query
> sequence, with each of
> them having more than one iteration. The parser reaches the end of file
> to
> determine the last_iteration of the last sequence instead of the
> corresponding last_iteration of
> each query sequence.

I am pretty sure you are correct that BPpsiblast.pm currently does not
correctly handle reports with multiple queries each having multiple
iterations.

If you (or anyone else on the list) would like to fix this, it would be
great.  Alternately, I will fix it when I can, but that may take a while
since I am pretty busy right now (I hope to have it fixed before the 1.0
release).  It would be helpful if you could send me a copy of the script
you are using and the psiblast report you are parsing.

Peter