Extracting subset of trees from trees file

[Brittany Rife]

This may be a silly question, but a previous coworker had combined BEAST .trees files in LogCombiner without resampling to provide a final file with 10,000 trees. Now the .trees file is too big for TreeAnnotator to handle to create the MCC tree, so I need to extract 10,000 trees from this gigantic file. I am not even sure how many trees is actually in this file. Does anyone know how to do this?

[Santiago Sánchez]

Hello Brittany,

This command line in the terminal will give you the exact number of trees in your tree file:

grep -c "tree STATE" $1 your_tree_file.trees

In addition, you can use this perl script I wrote to resample your large tree. Run it with the "-h" argument to get the details of how it works. It will be something like:

perl GetPosteriorTrees.pl -burnin 0 -resample 10000 -trees your_tree_file.trees -out  your_tree_file_resampled.trees -HPD false

Let me know if this works for you.

Cheers,

Santiago

2014-06-02 8:39 GMT-04:00 Brittany Rife <rife...@gmail.com>:

This may be a silly question, but a previous coworker had combined BEAST .trees files in LogCombiner without resampling to provide a final file with 10,000 trees. Now the .trees file is too big for TreeAnnotator to handle to create the MCC tree, so I need to extract 10,000 trees from this gigantic file. I am not even sure how many trees is actually in this file. Does anyone know how to do this?

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Santiago Sánchez-Ramírez

Department of Ecology and Evolutionary Biology, University of Toronto

Department of Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

Other email: santiago...@mail.utoronto.ca

Tel. 416-586-8025

[Santiago Sánchez]

I found a small bug in the script. Here is the corrected version.

[Brittany Rife]

Great! The only problem is that is not in the proper format for TreeAnnotator. Do you also have a small modifier script for the file?

[Brittany Rife]

Nevermind. I think it just stuck an "END;" after the taxon number assignment section that TreeAnnotator didn't like

[Santiago Sánchez]

Hi Brittany,

Here is a corrected version of the script.

Cheers,

Santiago