[Mesquitelist] MESQUITE scripting - opening character and tree files

[Wayne Maddison]

Let me see if I understand what you want.  You would like to open a 
file with matrix, then open a file with a tree, do a calculation, 
save the results to a file, then close both files, go on to the next 
matrix and tree, and so on?

Is the calculation done dependent on a tree window or not?  What 
exact calculation do you want done?

There is no problem reading a series of files via a script, but 
exactly how this should be done will depend on just what calculation 
you want.

Wayne

At 10:19 AM +0200 29.4.2009, Aidan Budd wrote:
>Hi MESQUITEers
>
>I'm trying to write MESQUITE scripts that will load trees stored in around
>100 different PHYLIP/NEWICK-format tree files, and binary character data
>(simple format) stored in the same number of external files (each of
>the 100+ trees is associated with one of the binary character
>datasets) such the appropriate tree/character-matrix pairs share the same
>taxa blocks
>
>The "trick" of doing the analysis via the MESQUITE GUI, and then looking
>at the MESQUITE scripting commands used to do the analysis doesn't work
>here - completely appropriately, MESQUITE simply writes appropriate taxa,
>tree, and charcter matrix NEXUS blocks based on the imported data, rather
>than specifying the script commands needed to reach this state.
>
>I'd greatly appreciate if someone could post an example script that would
>enable me to do something like this - I haven't been able to find an
>example to help me with this.
>
>Alternatively, perhaps this is just not feasible using MESQUITE, and I
>should rather put together a perl/python script that "simply" creates a
>NEXUS format file with appropriate tree/taxa/character-matrix blocks...?
>
>(Somehow it'd be a shame, though, if this were the way to do it - I'd
>rather avoid getting all the formating of these blocks right, parsing the
>input files etc.)
>
>Thanks
>
>Aidan
>
>--
>----------------------------------------------------------------------
>Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
>EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
>Meyerhofstr. 1, 69117 Heidelberg, Germany
>
>http://www.embl-heidelberg.de/~budd/
>http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
>
>
>
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-- 
--------------------------------------------------------
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: wmaddisn at interchange.ubc.ca   FAX: +1 604 822-2416

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