[Bioperl-l] Test related Suggestions

Chris Fields cjfields at uiuc.edu
Thu Jul 5 10:34:22 EDT 2007

On Jul 5, 2007, at 8:12 AM, Heikki Lehvaslaiho wrote:

> One more suggestion:
> It would be extemaly useful if we had a standard way of testing  
> that a when a
> file is read into a bioperl object and then written out again into  
> a same
> format, the input and output files are identical. If not, the test  
> should
> show where the the differences start (showing all the differences  
> would just
> clutter the screen).
> This standard method/subroutine should be used to test all sequence  
> and other
> text file IO.
> Any takers?
> 	-Heikki

I agree.  There are some 'round-trip' tests with genbank.t or SeqIO.t  
that do some checking, I think, but something like this would be of  
use.  However, what if the test file is old (as many in t/data are)  
and the format has changed?  GenBank and EMBL, for instance, have  
gone through several changes to format.


More information about the Bioperl-l mailing list