[Biophp-dev] Updates

[Serge Gregorio]

Hello all!

>>Nico: I'll try them out.  It might be a good idea to 
>> include some 'test' scripts`, as a demonstration <SNIP>

Yes, and it can attract the interest of "passers-by" 
to the project who might be too timid to actually look at the code.

>> Nico: and as a starting point for people to write >> their own scripts.

Yes, and the effort gives a lot of lessons in how
to continually improve the underlying codebase. For
instance, by writing the Amateur Gene Finder script,
I found out it was very tedious using GenePHP 1.0 
to work with individual codons.  And so, I promised
myself to make up for this inadequacy next release
by writing a bunch of methods like get_codon(), next_codon(), prev_codon(), etc.

>Sean: where these modules fit in the genephp scheme >of things so I can move them.

I think they can fit nicely into the I/O section that you and Nico are working on (Parsing being half of it).

>> Nico: seqIOWrite section, that would be great.  I >> am very busy doing real biology right now, and I 

Well, maybe you'd like to share a little about your "real biology" work?  That would be a welcome break from all the coding stuff we've been discussing 
the past few weeks.

Are you working on re-creating dinosaurs a la Jurassic Park? =)  Speaking of which, there's this guy I saw on Discovery channel who's actually doing that on preserved (fossilized?) microorganisms?  Cool!

>Sean: Serge - will you be doing any work on the seq >object over the next 7-10 days or so?  If not, I can >also e.g. add interface methods and perhaps one or ?>two other functions while I'm on the road and upload
>the changes when I get back.

I'm deep into the parsers right now.  You're welcome to add interface and other methods.  We (a.k.a. the "Design Committee") can all review them later on.   
  
Regards,

Serge


Need a new email address that people can remember
Check out the new EudoraMail at
http://www.eudoramail.com