[Bioperl-l] SeqIO::swiss->write_seq

[Jason Stajich]

On Fri, 29 Jun 2001, Ewan Birney wrote:

> On Fri, 29 Jun 2001, Elia Stupka wrote:
> 
> > > module depencies for future releases. I'd like to embrace external modules
> > > cautiously. Tie::IxHash is one I'd like to depend on which preserves the
> > > order items are added to a hash so that keys %hash returns the hash items in
> > > the order they were added in. If we are agreeded in adding this dependancy
> > > it will be trivial to preserve the tag order for a feature.
> > 
> > Jason and others, 
> > 
> > Tie:IxHash sounds great, let's not be too itchy about modules that can be
> > helpful, we are going to end up writing it in bioperl otherwise, don't you
> > think?
> 
> my view here is that we should be able to do this without requiring
> Tie::IxHash - the model implicitly has an array inside of it - not a hash
> - right for sequence features - I think we just need to quell any sorting
> going here. 
> 

okay - i can see this not being so important, we can always implement
ourselves if we think tag order is important (will be if we want to have
strict diffless output from/to SeqIO) but I suspect it will be a parallel 
array just like IxHash does.

While on the topic of external modules - I'd rather rely on
these modules rather than our reimplementation in Root::IO -
File::Spec, File::Temp, File::Path.

-Jason

> 
> I'll poke around a little.
> 
> 
> > 
> > Elia
> > 
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> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/