[Bioperl-l] Test related Suggestions
Nathan S. Haigh
N.Haigh at sheffield.ac.uk
Thu Jul 5 10:58:30 EDT 2007
Quoting Chris Fields <cjfields at uiuc.edu>:
> 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.
Is there any way to distinguish variants apart other than just layout? e.g. a version number of the likes?
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