Re: [Treebase-devel] Mesquite and trees without translation tables

[Wayne M. <wma...@in...>]

Dear Bill,

At 5:24 PM -0400 23.6.2009, William Halliday Piel wrote:
>Dear David and Wayne,
>
>As you know, TreeBASE is using a headless version of Mesquite to 
>parse all incoming data.
>
>I've noticed that although Mesquite is happy parsing a tree with a 
>translation table (but without a taxon block), for some reason it 
>doesn't like trees that lack a translation table and a taxon block.
>
>For these tree files (e.g. the default tree file produced by MrBayes 
>-- see attached), I get the following message:
>
>A block of trees has been read for which no corresponding block of 
>taxa has been found, and no block of taxa could be created for it. 
>If you had expected that the trees would have applied to an existing 
>block of taxa, it is possible that the taxa no longer correspond 
>because of changes in names or in which taxa are included.
>
>However, if a translation table exists, I get the following message 
>-- which is similar, but has a much happier outcome (i.e., the tree 
>gets parsed):
>
>A block of trees has been read for which no corresponding block of 
>taxa is available;  a new block of taxa has been created for it.  If 
>you had expected that the trees would have applied to an existing 
>block of taxa, it is possible that the taxa no longer correspond 
>because of changes in names or in which taxa are included.
>
>How is it that in one case a new block of taxa is created, but in 
>the other case "no block" could be created?

The translation table is easy to parse and reinterpret as if a taxa 
block.  Without a translation table, Mesquite is forced to invent 
taxa on the fly as it is reading a tree.  Not a pretty scenario...

We can look into a change to make this work; it will take some 
programming.  But I seem to remember we've done this sort of thing 
somewhere in the code.

Wayne

>
>Is there a workaround (e.g. a preferences flag?) that we can use so 
>that Mesquite will parse MrBayes tree files without taxon blocks?
>
>thanks,
>
>Bill
>
>
>Dear David and Wayne,
>
>As you know, TreeBASE is using a headless version of Mesquite to 
>parse all incoming data.
>
>I've noticed that although Mesquite is happy parsing a tree with a 
>translation table (but without a taxon block), for some reason it 
>doesn't like trees that lack a translation table and a taxon block.
>
>For these tree files (e.g. the default tree file produced by MrBayes 
>-- see attached), I get the following message:
>
>A block of trees has been read for which no corresponding block of 
>taxa has been found, and no block of taxa could be created for it. 
>If you had expected that the trees wo isting block of taxa, it is 
>possible that the taxa no longer correspond because of changes in 
>names or in which taxa are included.
>
>
>However, if a translation table exists, I get the following message 
>-- which is similar, but has a much happier outcome (i.e., the tree 
>gets parsed):
>
>A block of trees has been read for which no corresponding block of 
>taxa is available;  a new block of taxa has been created for it.  If 
>you had expected that the trees would have applied to an existing 
>block of taxa, it is possible that the taxa no longer correspond 
>because of changes in names or in which taxa are included.
>
>
>How is it that in one case a new block of taxa is created, but in 
>the other case "no block" could be created?
>
>thanks,
>
>Bill
>
>
>Attachment converted: Thrandina:RNF213IRBPMLLRhodomin3.zip 
>(pZIP/«IC») (00260B04)


-- 
--------------------------------------------------------
Wayne Maddison
  Professor and Canada Research Chair
          Depts. of Zoology and Botany and
          Biodiversity Research Centre
  & Director
          Beaty Biodiversity Museum
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

email: wma...@in...   FAX: +1 604 822-2416

Mesquite: http://mesquiteproject.org
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Tree of Life: http://tolweb.org
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Home page: http://salticidae.org/wpm/home.html