[Biopython-dev] Parsing TRANSFAC matrices with Bio.Motif

[Michiel de Hoon]

Hi Bartek,

OK, thanks!
I'll go ahead with the implementation then, and write an update to the mailing list again so people can have a look at it.

Best,
-Michiel.

--- On Sat, 10/27/12, Bartek Wilczynski <bartek at rezolwenta.eu.org> wrote:

> From: Bartek Wilczynski <bartek at rezolwenta.eu.org>
> Subject: Re: [Biopython-dev] Parsing TRANSFAC matrices with Bio.Motif
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Cc: "BioPython-Dev" <biopython-dev at biopython.org>
> Date: Saturday, October 27, 2012, 8:55 AM
> Hi Michiel,
> 
> On Sat, Oct 27, 2012 at 2:06 PM, Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
> 
> > Actually I was thinking about the suggestions for
> Bio.Motif I made earlier (see http://lists.open-bio.org/pipermail/biopython-dev/2012-September/009946.html).
> Right now they are just ideas, so I haven't implemented them
> yet. You mentioned in your reply last month:
> >
> >> I'll try to come up with a more thought through and
> longer response
> >> later in the week...
> >
> 
> Absolutely. It's just that I had quite a crazy time lately
> (time spent
> writing proposals and other such stuff...) and I didn't
> really think
> too much about Bio.Motif.
> 
> > So I was wondering if you have any additional comments
> on these suggestions, or if I can go ahead and start
> implementing.
> >
> 
> I'm sorry if my inactivity has slowed things down. I'll try
> to be more
> constructive this time.
> 
> I think that one thing clear is the Bio.Motif could use some
> code
> optimization, especially in the area of PWM searching.
> Honestly, I
> don't think that there will be a time in a forseeable future
> that I'll
> do it, so if you feel like implementing a better code for
> PWM
> handling/searching I'll be happy to do some code review or
> testing.
> 
> There are a few things I think would be good to keep:
> - possibility to invoke motif.pwm_search(...) without
> worrying about
> the fact that it is actually carried out by some specialized
> class
> - possibility to determine motif thresholds based on fpr or
> fnr as
> currently implemented in Bio.Motif.Thresholds module
> - possibility to convert count based motifs to PWM based
> motifs
> without much fuss...
> 
> All of these things are not really in conflict with your
> idea of
> moving the PWM related code to the special class, so if you
> want to do
> that, go ahead.
> 
> If you also have trouble finding time to implement these
> improvements,
> I could try to recruit some master student from our
> department to do
> that. But if you have time to do the implementation
> yourself, it will
> probably be better and faster that way.
> 
> best
> Bartek
> 
> -- 
> Bartek Wilczynski
>