[Bioperl-l] bugs #927 and #949 (BPbl2seq, BPlite)

Hilmar Lapp hilmarl@yahoo.com
Tue, 24 Apr 2001 11:14:06 -0700

In order to be able to address these bugs properly we need sample
files for reproducing the cases, and before one of the developers
will spend time on making up samples we'll rather down-prioritize
these bugs. Ann seems to be unavailable or busy; if anyone else on
the list happens to have a suitable sequence and corresponding
Blast/bpl2seq report around, please submit to me, otherwise these
bugs will remain unfixed for the next point release.

Bug #927 is about BPbl2seq choking on a report with no alignment.
Bug #949 is about BPlite having problems when a subject has HSPs
on the plus and minus strand (in blastx).

The latter BTW is certainly going to pose a problem: the subject
is a SeqFeatureI and you'll want to know the strand for it. If the
frames of the HSPs don't agree on the strand, which strand do you
assign to the subject?

Hilmar Lapp                              email: hilmarl@yahoo.com
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757