[Biopython] Combine nexus files but not concatenating them

[Peter]

On Thu, Oct 8, 2009 at 12:23 AM, Denzel Li <denzel.dz.li at gmail.com> wrote:
> Hi Peter:
> Regarding the Nexus datatype supported in Bio:Nexus:Nexus, I mean nexus like
> the following, where the datatype is a "mixing" of "standard" and "DNA".
> According to the function Bio:Nexus:Nexus._format (line 696), these
> datatypes are not supported yet. I am just wondering does the team has the
> plan to support these data types.

Oh right - in in your example, the digits encode morphology, but they could
also be phenotypes, or some other characteristic like gene copy number.

As to Bio.Nexus supporting this, hopefully Frank or Cymon can comment.

If Bio.Nexus did support this, then from the Bio.AlignIO point of view, with
the current object structure we'd have to use a sequence object (holding
both the digits, and the DNA) for the sequence strings (e.g. for s1 in your
example, Seq("10010ACGT")) with a generic single letter alphabet. This
would lose the fact that the first five characters are digits, but the rest are
DNA. This isn't ideal, and would probably cause trouble for Nexus output
(writing such alignments).

Would you want to try and deal with such "mixed" alignments via the
Bio.AlignIO interface?

Peter