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

[Donald G. Jackson]

Thanks, that fixed it.

Sorry for not checking CVS before sending off the email.  My brain's not 
working this afternoon.

Don

Jason Stajich wrote:

>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
>  
>