[Bioperl-l] potential Bio::SeqIO/ addition ? Inline::C usage??

[Aaron J Mackey]

On Thu, 20 Jun 2002, Ewan Birney wrote:

> As long as the main modules (Bio::Seq, Bio::SeqIO) don't end up having a
> dependancy on Inline::C, I see this as being much like XML::Twig
> dependancies etc...

It would only be Bio::SeqIO::tzf.pm, ::abi.pm, ::exp.pm, etc.  And they
should politely fail if you try to use them without having either the
io-lib library installed, or if Inline::C wasn't available (although Brian
Ingerson is promising that the next version of Inline will allow modules
to be packageable such that Inline itself is not required on the
destination machine, so things can only get better).

The io-lib also contains code to read SCF files ... since we have a
pure-perl SCF SeqIO module, we have a few choices:

a) stick with the pure perl only solution
b) drop the pure perl module and use io-lib
c) use io-lib if available, or fallback to the pure-perl module (make the
pure perl module available directly by some other name: scfPP or
somesuch).

I think c) makes the most sense, of course, but is also the most work ;)

Any bioperl lurkers out there who want to do some Inline::C wrapper work?

-Aaron
-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu