Writing a for loop for treepl?

[dylanHco]

Writing a for loop for treepl?

[dylanHco]

Hi Joseph,

Thank you so much for this! I tried both, but in the end the second method worked for me.

[josephwb]

If you are using the same config file for all the trees (say, trees from a common bootstrap or posterior distribution), this will work:

#!/bin/bash

# assumes:
# 1. a single treePL config file 'treepl.config' for all trees
#    - this assumes that all settings are the same
#       - constraints, mrcas, smoothing parameter, etc.
# 2. the tree filename specified in the config file is 'test.tre'
#    - do not set an output file name. we will use the default of 'out_dates'
# 3. there is an existing directory called 'complete'

for f in *.tre; do
  # copy current tree into 'test.tre'
  cp $f test.tre
  
  # run treePL
  treePL treepl.config
  
  # rename and move results
  mv out_dates.tre complete/"${f%.*}".dates.tre
  mv out_dates.tre.r8s complete/"${f%.*}".r8s.tre
  
done;

# get rid of test.tre to clean up
rm test.tre

put the above code in a text file called run_multi.sh and do:

chmod 755 run_multi.sh

to make it executable.
Make sure the output directory complete exists in the directory with the trees and single config file, and do:

./run_multi.sh

If you have separate config files for each tree, make sure they do have output file names specified (if not, one result will just overwrite the previous). Everything (tree and config files) can reside in the same directory, and then your bash script would simply be:

#!/bin/bash

for f in *.config; do
  treePL $f
done;

HTH.