Bio::Seq (fwd)

Georg Fuellen
Tue, 18 Feb 1997 13:02:24 +0000 (GMT)

Forwarded message:
From: "Steve A. Chervitz" <sac@genome.Stanford.EDU>
Date: Mon, 17 Feb 1997 18:21:36 -0800 (PST)
To: Georg Fuellen <fuellen>


Thanks for taking a look at my new site and adding a link to it on your 
page. My stuff is not as far along as yours. Maybe this will provide 
some motivation for enhancements!

> (btw, how would you like to be addressed, given that I don't
> want mixups between Steve(n) Brenner and you ? SteveC? Steve Ch.?
> versus SteveB / SteveBr / Steve Br. (???, advice please!) )

SteveC is fine. 

> I would *very much* appreciate any and all comments on Bio::Aln,
> same as Chris Dagdigian for Bio::Seq.

I'll keep you informed as I work on integrating your modules with mine.

> 3) Is the %names hash in Bio::Aln sufficient for the moment to hold db, 
> prog, etc ? Or would you like to see individual accessors ?

I would favor individual accessors.

> 5) I'm unclear about the Sacch stuff, and the stuff below GeneSeq.
> I think this doesn't matter, though.

The Sacch modules are for creating yeast-specific derivatives of the 
Bio::Chrm, Bio::Gene, and Bio::Protein modules. The Sacch:: versions 
include code that is not portable to other organisms and file systems. 
I've tried to abstract out the generic features of these biological 
objects into the Bio:: classes. However, I can't vouch for how truly 
universal these objects are at present since I've created only the 
features needed to solve particular problems. I'm sure there are things  
I've missed. 

(Note: my modules are actually in the "Bio2" and "Sacch2" directories. 
This is a developmental artifact which I'm intending to correct so that 
they will be in Bio:: and Sacch::.)

> Regarding the ``Programming Style Conventions for Bioperl Modules''
> I've followed the recommandations in the ``Module List'', especially
> ``Function and method names seem to work best as all lowercase. E.g.,
> $obj->as_string().'' Anyway, now that people are testing the Aln & Seq 
> code, it's (almost) too late to make changes like introducing 
> upper-case for methods. Also, I've definitly become a fan of merging
> accessor and modifyer into one function.

I must apologize for the lack of consistency in my code at present. My 
earlier code had methods starting with an uppercase but I have 
been trying to phase this out since in the OO world, an uppercase first 
character is used for class names. Also, method calls are very 
frequent; having them lowercase improves usability. The one method 
naming convention I do like is having all internal methods start with an 
underscore. This makes it easy to identify the public interface. 
I've been gradually phasing this into my code.

> I've printed out your Molecule and Blast classes and will read thru them
> in a few days; for which other texts would you recommand closer inspection ?

The Blast module uses and, which you might want to look 
at in conjuction with and show 
some of the work I did with sequences. However, I haven't used them in a  
while, so the code needs updating, especially for integrating with 
> If possible, let's send most email to 
> so that it's archived, and seen by everyone involved.
> *May I bounce this email to vsns-bcd-perl ?*

Sure. I'll let you bounce the previous message as well as this reply (so 
the messages appear in sequence).

Best Regards,