[Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Nov 16 01:07:21 EST 2008


------- Comment #5 from cjfields at bioperl.org  2008-11-16 01:07 EST -------
(In reply to comment #4)
> (In reply to comment #3)
> > Do you think we should just be also storing absolute identity and similarity
> > numbers for the HSPs too and have the frac_identity and frac_similar as
> > computed values?  I can't remember why I went with storing the fraction numbers
> > only although if you want the actual values you can also get from seq_inds
> > method too (for cases when the alignment string data is available).
> We could store abs. identity, similarity or other bits explicitly reported from
> the HSP block, then calculate other bits on the fly.  I think it is a nice
> metric to recalculate a few things for sanity (eg. % ID, conserved) to ensure
> other calculations make sense, but we could maybe do that lazily (in fact,
> Sendu has already largely refactored GenericHSP so that most calculations are
> lazily computed).

See bug 2663.

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