[Treebase-devel] Fwd: reading nexus file from treebase?

[Hilmar L. <hl...@ne...>]

FYI - the NEXUS download from TreeBASE seems to contain stuff that  
aren't understood by some (rather widely used) NEXUS parsers. I don't  
know whether these are part of the core standard or were added later  
as a "flavor", but it may be beneficial to get rid of them if they  
aren't crucial.

Thoughts?

(BTW the readNexus() function in the phylobase package - which can  
read this - is based on NCL. So presumably that means that in NCL's  
implementation of the standard this is correct. It's just that not  
everyone uses NCL :-)

	-hilmar

Begin forwarded message:

> From: Emmanuel Paradis <Emm...@ir...>
> Date: March 25, 2011 12:00:36 AM EDT
> To: François Michonneau <fra...@gm...>
> Cc: R-s...@r-...
> Subject: Re: [R-sig-phylo] reading nexus file from treebase?
>
> Scott,
>
> readNexus (phylobase) can read your tree but not read.nexus (ape).  
> The problem is the two lines inserted within the TREES block:
>
> BEGIN TREES;
> TITLE Tb10793;         <<<<<<
> LINK TAXA = M4787;     <<<<<<
> TREE Fig._3c = [&R]
>
> If you delete them, it's OK. FigTree also cannot read this file.
>
> Cheers,
>
> Emmanuel
>
> François Michonneau wrote on 25/03/2011 00:35:
>> Hi Scott,
>>  Which version of phylobase are you using and which architecture? I  
>> can
>> read the file on my machine.
>>  Cheers,
>>  -- François
>> On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain <myr...@gm... 
>> >wrote:
>>> Hello,
>>>
>>> I can't get read.nexus (ape) or readNexus (phylobase) to read  
>>> nexus files
>>> downloaded from treebase with URLs parsed from xml files. I can't  
>>> manually
>>> edit each file as I want to read a lot of these files. Is there an  
>>> easy fix?
>>> One of the files is copied below.
>>>
>>> Thanks!
>>> Scott Chamberlain
>>> Rice University, EEB Dept.
>>>
>>>
>>>
>>>
>>> #NEXUS
>>>
>>> [!This data set was downloaded from TreeBASE, a relational  
>>> database of
>>> phylogenetic knowledge. TreeBASE has been supported by the NSF,  
>>> Harvard
>>> University, Yale University, SDSC and UC Davis. Please do not  
>>> remove this
>>> acknowledgment from the Nexus file.
>>>
>>>
>>> Downloaded on March 24, 2011; 16:32 GMT
>>>
>>> TreeBASE (cc) 1994-2008
>>>
>>> Study reference:
>>> Brown R., & Yang Z. 2010. Bayesian Dating of Shallow Phylogenies  
>>> with a
>>> Relaxed Clock.
>>> Systematic Biology, 59(2): 119-131.
>>>
>>> TreeBASE Study URI:
>>> http://purl.org/phylo/treebase/phylows/study/TB2:S10165]
>>>
>>> BEGIN TAXA;
>>> TITLE M4787;
>>> DIMENSIONS NTAX=16;
>>> TAXLABELS
>>> Chalcides_coeruleopunctatus_E2806.20
>>> Chalcides_coeruleopunctatus_E2806.22
>>> Chalcides_manueli_E2506.1
>>> Chalcides_mionecton_mionecton_E2506.10
>>> Chalcides_mionecton_mionecton_E2506.12
>>> Chalcides_mionecton_trifasciatus_E2506.18
>>> Chalcides_polylepis_E14124.1
>>> Chalcides_polylepis_E14124.2
>>> Chalcides_polylepis_E2506.21
>>> Chalcides_sexlineatus_bistriatus_E2806.6
>>> Chalcides_sexlineatus_sexlineatus_E2806.8
>>> Chalcides_simonyi_E3007.2
>>> Chalcides_sphenopsiformis_E8121.26
>>> Chalcides_sphenopsiformis_E8121.27
>>> Chalcides_viridanus_E2806.10
>>> Chalcides_viridanus_E2806.14
>>> ;
>>> END;
>>>
>>> BEGIN TREES;
>>> TITLE Tb10793;
>>> LINK TAXA = M4787;
>>> TREE Fig._3c = [&R]
>>> ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21)))))));
>>> [! TreeBASE tree URI:
>>> http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136]
>>>
>>>
>>> END;
>>>
>>>
>>>       [[alternative HTML version deleted]]
>>>
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>>> R-sig-phylo mailing list
>>> R-s...@r-...
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>>
>> 	[[alternative HTML version deleted]]
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>
> -- 
> Emmanuel Paradis
> IRD, Jakarta, Indonesia
> http://ape.mpl.ird.fr/
>
> _______________________________________________
> R-sig-phylo mailing list
> R-s...@r-...
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-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================