[BioPython] Alphabet Checking

[Tiago Antão]

On Jan 28, 2008 5:56 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > Aren't those two exactly equal?
> >
> > Matching references doesn't seem to work as expected :(
>
> That does look like a bug...

It is probably completely unrelated, but it might not...

>From an "helicopter view" at the code I have noticed that SeqIO uses
Nexus in some cases.

I have patched a previous Nexus bug by using deepcopy, which could
cause something like this:

AssertionError: cannot translate from given alphabet (have
IUPACAmbiguousDNA(), need IUPACAmbiguousDNA())

(ie, it has the same type name, but is really not the same object)

Again, it is probably unrelated (I know very little about Bio.Seq and
Bio.SeqIO), but, just in case...