[Bioperl-l] BPlite and frames

Hilmar Lapp hlapp@gmx.net
Sat, 25 Aug 2001 14:33:52 +0200

Thanks to Roger's recent fixes BPlite can now handle/decode the
frame information properly. However, there's now a problem with
the other BLAST flavours, because BPlite::Sbjct and BPlite::HSP
are now expecting the parent object to know about a BLAST_TYPE
member variable, which it doesn't for bl2seq reports and
apparently neither for PSIBlast/PHIBlast.

It appears that at least bl2seq reports do not contain any
information about the "program" that was used (you have the same
palette to choose from: blastn, blastx, etc). Does anyone know
whether this was changed in the latest versions (I have 2.1.3

Also, does anyone already know whether it is safe to assume that
for PSIBlast you always have a protein query (and DB)? I.e. frame
does not apply?

The AlignIO test spits out warnings related to this same problem,
too. If I have time I'll investigate.

Finally, I see a problem there regarding memory chains (not a
cycle though), as Sbjct.pm and HSP.pm keep a pointer to the parent
object (Tools::BPlite instance). I.e., if you dispose of a
Tools::BPlite object, the corresponding file will not be closed
until you dispose of all related BPlite::Sbjct and BPlite::HSP
objects. Not sure whether we want to accept this.

Hilmar Lapp                              email: hilmarl@yahoo.com
A-1120 Vienna