[Bioperl-l] Modifying Blast.pm problems

Jason Stajich jason@chg.mc.duke.edu
Tue, 27 Feb 2001 18:32:37 -0500 (EST)

Hi Terry.

The beast that is Blast.pm is not really being maintained right now as we
have been migrating code away from it and the original developer doesn't
really have time to work on it any more.  

Can you tell us which version of bioperl you are using.  Have you tried
Bio::Tools::BPlite (available only in recent release of bioperl) - does it
meet your needs?  Adding this functionality to BPlite is LOADS easier than
messing with Blast.pm as you have probably found hitting you head against
this wall.  There are long term plans to phase it out and move all the
functionality into a simplier to maintain blast parsing module but I know
that doesn't help you solve your problem you are working on right now...


On Tue, 27 Feb 2001, 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 ?
> thanks,
> terry
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Jason Stajich
Center for Human Genetics
Duke University Medical Center