[Bioperl-l] Modifying Blast.pm problems

Mark, Terry tmark@amgen.com
Tue, 27 Feb 2001 15:06:49 -0800

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 ?