[Bioperl-l] Modifying Blast.pm problems

Hilmar Lapp lapp@gnf.org
Tue, 27 Feb 2001 15:32:08 -0800

"Mark, Terry" wrote:
> Hi all,
> I need to be able to determine the effective database length used in NCBI
> Blast reports.
> Since Blast.pm does not have this functionality, I happily set about writing
> a few lines at the very end of _set_blast2_stats to parse this information
> and save it in a new property,
> $self->{_effective_length_db}.  The accessor I wrote failed, however, and I
> cannot understand why.
> My property _effective_length_db *is* being set properly in
> _set_blast2_stats, and it *is* still set and visible in the (calling
> routine) _parse_footer.
> However, it seems that IMMEDIATELY after _parse_footer returns to (its own
> caller) _parse_alignment, _effective_length_db is now undef'd.
> I have been driving myself crazy trying to figure this out, and wondered
> (though I really doubt it) whether my problem is related to some chicanery
> in the code that I might be unaware of.
> Of course the other possibility is that I am doing something really stupid,
> but what I have done really amounts to a single line of code at the end of
> _set_blast2_stats, limiting what I could have done wrong, and the property
> does seem to be set afterwards...
> Does anybody have any insight into what might be happening ?  Has anybody
> had similar problems trying to modify _set_blast2_stats ?

I have no idea what might be happening there. Blast.pm somewhere keeps
a static object, maybe this interferes, but that's only a very vague

If you've got a few minutes more time (well, maybe a few hrs, but
shouldn't take that long), I'd rather like to encourage you to enhance
BPlite with this functionality. Our problem with Blast.pm is that it's
a beast which no-one presently maintains, in contrast to BPlite.

If you're using Bioperl 0.6.2 you'll need to obtain the present
development tree from anonymous CVS, because BPlite wasn't part of
0.6.2. The development tree is pretty stable at the moment and shaping
up to become the 0.7 release code.

Sorry I couldn't help more :)

Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757