[Biopython] Biopython 1.65 post-install test - get different result on one line

[Peter Cock]

On Sun, Mar 15, 2015 at 12:54 AM, John DeFilippo
<sarchasm.1357 at gmail.com> wrote:
> In Biopython Installation (http://biopython.org/DIST/docs/install/Installation.html)
> #6 -  Making sure everything worked
>
> 5th line of python code
> new_seq.translate()
>
> gives output as
> Seq('DQK', HasStopCodon(IUPACProtein(), '*’))
>
> but I get
> Seq('DQK', IUPACProtein())
>
> Does this indicate something wrong with my install?
>
> Thanks

No, there is nothing wrong with your installation. I get the same
here. It seems the code has changed slightly since that example
was written, probably this change back in 2008:

https://github.com/biopython/biopython/commit/b135d280e0ff66cbc503a7344a55496b123afdf3

The current translation code doesn't bother to add the
"HasStopCodon" stuff unless the translated sequence
actually has a stop codon ("*") in it.

I've updated the installation document for our next release:

https://github.com/biopython/biopython/commit/7cc8bc97510f57ef1b163f5b470fc4e8fceb2189

Well spotted - thank you!

Peter

Note to self: We should probably extend the code in
test_Tutorial.py to cover the other LaTeX files like this
installation file?