[Biopython-dev] Bio.Nexus and internal node labels (Bug 2788)

[Nick Matzke]

Peter wrote:
> On Mon, Jul 20, 2009 at 8:13 PM, Nick Matzke wrote:
>> Hi all, here is my weekly update...
>>
>> 1. Bug fix on Nexus.Tree class is working well so far.  Thanks Brad!!
>>
> 
> Cool. I haven't tried it personally though ;) Frank and/or Cymon - any
> comments regarding Brad checking this in? See Bug 2788 for details.
> 
> I gather you (Nick) are using this on ultrametric Newick trees

yes

  - could
> you supply a sensibly sized example to use as a unit test? Initially
> this can be just to test Brad's patch to Bio.Nexus, but try and pick
> something you can build documentation examples around in future.




This is probable a reasonable size, a subset of my bigger tree.  (Just 
gymnosperms; times are in millions of years.)

(((((Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)TT1:25.000000)Taxaceae:90.000000,((((((((Calocedrus:85.000000,Platycladus:85.000000)CP:5.000000,(Cupressus:85.000000,Juniperus:85.000000)CJ:5.000000)CJCP:5.000000,Chamaecyparis:95.000000)CCJCP:5.000000,(Thuja:7.870000,Thujopsis:7.870000)TT2:92.13)CJCPTT:30.000000,((Cryptomeria:120.000000,Taxodium:120.000000)CT:5.000000,Glyptostrobus:125.000000)CTG:5.000000)CupCallTax:5.830000,((Metasequoia:125.000000,Sequoia:125.000000)MS:5.000000,Sequoiadendron:130.000000)Sequoioid:5.830000)STCC:49.060001,Taiwania:184.889999)Taw+others:15.110000,Cunninghamia:200.000000)nonSci:15.000000)Tax+nonSci:10.000000,Sciadopitys:225.000000):25.000000,(((Abies:106.000000,Keteleeria:106.000000)AK:54.000000,(Pseudolarix:156.000000,Tsuga:156.000000)NTP:4.000000)NTPAK:24.000000,((Larix:87.000000,Pseudotsuga:87.000000)LP:81.000000,(Picea:155.000000,Pinus:155.000000)PPC:13.000000)Pinoideae:16.000000)Pinaceae:66.000000)Coniferales:25.000000,Gink
go:275.000000)gymnosperm:75.000000;

I am using this as a test case in my own script, I have put some effort 
into reading up on Unittest but I don't quite get how it all fits 
together yet.


Another important case I will try and come up with is the results of 
pruning a tree, in my experience it is very easy to mess up the tree 
and/or branchlengths when pruning.



> 
> Thanks,
> 
> Peter
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
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