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

[Bartek Wilczynski]

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