[Bioperl-l] $hit_object->frac_aligned_hit/$hit_object->frac_aligned_query

Bernd Brandt bernd.brandt at gmail.com
Wed Aug 2 14:49:20 EDT 2006


Hi,

"frac_identical and frac_conserved can still be very wrong"
They were wrong with hmm report parsing (hmmsearch). The  bioperl-live
(CVS 14 July 2006) returned 0 for both fracions. I will check it with
the newest CVS and send a small test script.

Regards,
Bernd

On 8/2/06, Sendu Bala <bix at sendu.me.uk> wrote:
> Hilmar Lapp wrote:
> >
> > On Aug 2, 2006, at 7:23 AM, Sendu Bala wrote:
> >
> >> It should be noted that all frac_* statistics and probably others from
> >> hit objects have had a high chance of being wrong in the past, and
> >> frac_identical and frac_conserved can still be very wrong*. It would be
> >> a good idea if someone were to make these methods return slightly more
> >> sane numbers.
> >>
> >> [*] which is to say, more wrong than you might reasonably expect, given
> >> the limitations with gapped or alignment-free blasts
> >
> > Can you elaborate? Specifically, can you put in tests that show the
> > wrong results?
>
> I've added some new tests based on Andreo's blast result, but atm I've
> left the tests commented out. See line 882 of t/SearchIO.t revision 1.94
> - a sane result would be less than 1.
>
> I think it ought to be possible to get better answers, but I got the
> feeling the fix wouldn't be completely trivial so I let it go, not
> having the time to spare right now.
>
> The reason I don't just call this a bug and make a bug report is that
> the documentation acknowledges that you won't always get a good answer,
> so it needs to be investigated if the current answer really is the best
> that can reasonably be given, or if there is some bug making the answer
> worse than it needs to be (as was the case with frac_aligned_hit and
> frac_aligned_query).
>
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