Bioperl: Re: bioperl-ext Patch for extension portability (fwd)

[Allen Smith]

On May 10,  7:20am, Ewan Birney wrote:
> On Wed, 10 May 2000, Allen Smith wrote:
> 
> > 
> > P.S. Incidentally, I realize that this extension is essentially a
> > direct port of part of WISE, without changes beyond those needed
> > to get it to run with Perl. It looks like my Ph.D. thesis is going
> > to be partially concerned with alignments and doing variations on
> > how to run them. Would there be interest in my (heavily) revising
> > the C code in this to integrate it more fully with Perl (e.g., to
> > have matrices entered through perl instead of external files),
> > and/or introducing another alignment package module using C code
> > from another public-domain source?
> 
> 
> Definitely (!).

Excellent.

> You could do this by hacking that code, or by hacking
> WISE.

I'm a bit more likely to do the former, since I'm much better at Perl
than at C - part of what I'd be doing is simplifying things by moving
functions from C into Perl.

> WISE is a pretty intertesting set of algorithms written by someone
> who only vaguely grasped proper library design and software
> engineering.

As someone who isn't a computer programmer by training, I fully
understand, believe me.

> In particular it based around a code generating langugage, called
> Dynamite, which can only be described as ... interesting ...

Umm... yes, I'd have to agree with that description. The levels of
functions-inside-very-short-functions that it seems to have generated,
for instance...

> 	a) rewrite/do your own thing looking at the WISE port for help
> 
> 	b) hack wise that comes in bioperl-cext

One and/or the other of these two look pretty likely... I am
interested in putting in the ability to do a DNA/protein matching with 
allowing for frameshifts, either via putting in estwise's code or
using that from Lars Arvestad, who I'm also in contact with.
	
	Thanks,

	-Allen

-- 
Allen Smith				easmith@beatrice.rutgers.edu
	
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