[Bioperl-l] Bio::Score of interest?

Cook, Malcolm MEC at stowers-institute.org
Tue Jun 27 12:01:45 EDT 2006


For the use case of TFBS analysis demonstrated in the attachment to the
bug, I would expect to find potentially three scores, ala, {evalue,
bitscore, and percentmatch}.  To deal with this in existing framework
(i.e. GFF/bioperl analysis modules/TFBS), I would try to make GFFx eat
scalars as scores and pack the three values into a string and unpack
them as needed for sorting, etc.  Else put the one score I know I'm
going to 'use' in a particular analysis into 'score' and adorn column 9
with the rest.

All this semantic cruft is overkill for a moving target and will never
settle down until your analysis results are no longer relevant.

my $.02

--Malcolm


>-----Original Message-----
>From: bioperl-l-bounces at lists.open-bio.org 
>[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sendu Bala
>Sent: Tuesday, June 27, 2006 5:22 AM
>To: bioperl-l at lists.open-bio.org
>Subject: [Bioperl-l] Bio::Score of interest?
>
>Please see http://bugzilla.bioperl.org/show_bug.cgi?id=2033
>Is the idea of a Bio::Score of interest? See bug, but basically an 
>object that can handle multiple kinds of scores effectively.
>
>I would like to use such a thing in Bioperl, but what standard 
>needs to 
>be met before Bioperl gets a new kind of object?
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