[Bioperl-l] GenBankParser comparison to bioperl parser

[Ewan Birney]

On Thu, 12 Sep 2002, Ian Korf wrote:

> I'll de-lurk for this.
> 
> I, for one, think that a bio-util-perl project would be a good 
> idea. Not everyone wants or needs the whole of bioperl. 
> Sometimes, a small utility outside the framework is useful. 
> Analogously, I use a full-featured text editor that counts 
> letters, words, paragraphs etc, but I still find myself using wc 
> from time to time.
> 
> I think that if something is going to be part of bioperl, it 
> ought to have the same consistent interface. But I like what 
> John has done, both at the interface and implementation level. 
> Is it possible to leave John's parser the way it is and offer a 
> bioperl interface to it?


This was my view (putting this as a skeleton below bioperl), but I am wary
of this actually mainly because I am not that compontent at the perl
magic level and so I am worried about the hooks and about maintance...


A naive bioperl implementation ontop of John's stuff would require loading 
the parser up with everything and then pulling into objects, which is 
fine, and would work - probably faster than current bioperl but certain 
this speed improvement should be achievable in the current bioperl parser 
as they are doing the same thing - it is just that we have crappy code 
probably down there. I will investigate. 


A cleverer wrapper would expose just that little more of "registered tags" 
of John's stuff and utilise the on-demand parsing call that John has 
implemented.


I like the bioperl-util repository - "for professionals only" I think it 
keeps diversity without freaking newbies out and we can trade code.


++ from me.