[Bioperl-l] Re: Problem with Bio::TreeIO::nexus

[Jason Stajich]

I have put a bunch of fixes in since revision 1.3.  I would suggest
getting the latest from CVS. If you want a patchfile to upgrade from
1.3 although it should be easy to grab from CVS I hope.

If it still doesn't work let us know.

----------------------------
revision 1.7
date: 2004/06/29 16:55:13;  author: jason;  state: Exp;  lines: +3 -4
back out attempted MrBayes parsing patch - shouldn't be needed; #1619
----------------------------
revision 1.6
date: 2004/06/24 15:14:07;  author: jason;  state: Exp;  lines: +8 -2
bugfix for #1656
----------------------------
revision 1.5
date: 2004/03/19 18:05:11;  author: jason;  state: Exp;  lines: +3 -3
handle nexus trees a little better I hope - more testing needed
----------------------------
revision 1.4
date: 2004/03/09 20:12:05;  author: jason;  state: Exp;  lines: +28 -28
some cleanup- wasn't matching all nexus formats
----------------------------


On Wed, 7 Jul 2004, Donald G. Jackson wrote:

> Jason or another TreeIO wizard,
>
> I'm having trouble reading in a nexus treefile created with Paup4b10.
> I've attached my code and an example treefile.  Briefly, when I call
> next_tree() I get no trees back.
>
> It looks as though the comment-counting mechanism is getting thrown off
> (Bio::TreeIO::nexus lines 124ff).  Once the opening comment closes, the
> module stops reading any data ;(.   I'm using version 1.3 of
> Bio::TreeIO::nexus
>
> I'd appreciate any suggestions or assistance.
>
> Thanks,
>
> Don Jackson
> BMS Bioinformatics
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu