[Bioperl-l] Test related Suggestions

Nathan S. Haigh n.haigh at sheffield.ac.uk
Thu Jul 5 09:47:24 EDT 2007

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

Wouldn't this require info about the formatting of the file to be stored 
in the object as well, such that the same formatting could be used when 
writing the file?

Wouldn't a better approach be to read the contents of file1 into ojb1, 
write obj1 to file2 in the same format, and then read file2 into obj2 
and compare obj1 to obj2 to ensure we have all the same data.


More information about the Bioperl-l mailing list