[Bioperl-l] Test related Suggestions
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
> 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?
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