[BioRuby] Bio::Assembly

Pjotr Prins pjotr.public14 at thebird.nl
Thu Jul 8 13:13:03 UTC 2010

Glad to see this excitement :). 

On Thu, Jul 08, 2010 at 01:24:41PM +0100, Anthony Underwood wrote:
> > How closely does BioRuby like to follow the BioPerl API?

Not. Though you wouldn't be the first to copy stuff.

> > I've noticed that BioRuby seems to handle file formats differently than
> > BioPerl, with most of them being in Bio::db/.  Can anyone expand on this?
> > 
> > Is there any place I can read about the best practices for BioRuby.  For
> > example, I haven't seen any instances of using hashes to pass parameters in
> > method calls e.g.
> > a.parse( :file => file, :format => format )

I am sure it is used and it is fine, when used for 'setting' options.
Only risk is that you lose checking of the number of parameters
passed. Which can lead to bugs.  Otherwise I like it for being
explanatory in the calling code.

Mind: It can lead to 'rich' interfaces - so common in R, where one
method handles many circumstances. These rich methods tend to be
really ugly and hard to test (=hard to prove correct). Don't use it to
replace multiple methods. Methods also are explanatory in the calling

> > Is this frowned upon in BioRuby?

I don't think so. But use it when it makes sense.


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