[Biopython] Combine nexus files but not concatenating them

[Denzel Li]

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.
------------
# Nexus
Begin data;
    Dimensions ntax=2 nchar=1000;
    Format datatype=mixed(Standard:1-5,DNA:6-1000) interleave=yes gap=-
missing=?;
    Matrix
[morphology]
s1 10010
s2  20011
s3  20010
s4  10020
[Gene 1]
s1 ACGT
s2 AAGT
s3 ACGA
s4 ACGT
...
; end;
---------------

Best,
Denzel

On Wed, Oct 7, 2009 at 5:29 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Wed, Oct 7, 2009 at 4:22 AM, Denzel Li <denzel.dz.li at gmail.com> wrote:
> > Hi Peter:
> > Thank you for the help. Both functions work well. By the way, will
> > "standard" datatype or "mixed" datatype be supported in Bio:Nexus:Nexus?
> >
> > Best,
> > Denzel
>
> Hi Denzel,
>
> I CC'd the list - please try and keep replies send there.
>
> I'm glad Bio.Nexus is working well for you.
>
> Regarding the finer details of the NEXUS file format and the Biopython
> code, I am not an expert - we need Frank or Cymon to comment. If
> you could give us a couple of examples of what you are asking for it
> would probably be much clearer (to me at least).
>
> Regards,
>
> Peter
>