[Bioperl-l] GenBankParser comparison to bioperl parser

[Ewan Birney]

On Thu, 12 Sep 2002, Elia Stupka wrote:

> >    - diversity of implementations in main repository good for pros and
> > experts to look at everything, see what is going on
> > 
> >    - diversity of implemetnations in main repository bad for newbies who
> > just get down right confused
> 
> Would a newbie doc file as well as pointers in each parser to the other
> parser and explanation do the trick in this specific case?
> 


Hmmm. I've looked at John's code - it is very nice and well layed out, but 
it is a big ish code base (naturally) uses deepish perl magic straight off 
the GenBank keys (which is a fine choice, but not to my taste, but I am 
one of those trad I'm-really-a-C-programmer Perl programmers so YMMV).


I vote --- we congratulate John on a job well done, point it out - link to 
it perhaps but actually do some deep thinking on our own parser first 
before anything drastic. 


Let me put it another way - I *will not* maintain this code down the 1.2 
branch ;). Elia - if you are up to fielding all bugs and questions (or if 
John is) then - more doable. My vote is still to keep it seperate...






> Elia
> 
> > 
> > 
> > Best solution - implementation that works in all cases, is easy to 
> > understand for newbies, powerful for pros, no performance issue, and 
> > *makes* the coffee.
> > 
> > 
> > Hmmm... thinking
> > 
> > (dangerous) look at adding it in as an underlying skeleton parser below
> > "SeqIO::genbank" into something like SeqIO::Raw::genbank and then move
> > SeqIO::genbank on top of that. This way people can drop down to "raw"
> > genbank mode.
> > 
> > 
> > 
> > John - would you be ok with this? I'll take a look at the feasibility of 
> > this...
> > 
> > 
> > 
> > 
> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>. 
> > -----------------------------------------------------------------
> > 
> 
> Elia
> 
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel:    +65 6874 1467        *
> * mobile: +65 9030 7613        *
> * fax:    +65 6779 1117        *
> ********************************
> 
> 
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------