Ruby script to restart BEAST runs. This constructs a new XML control file from the original control file and the last logged parameter values.

beast_checkpoint.rb

#!/usr/bin/ruby

# Designed to allow checkpointing of BEAST output files
# Input: beast_analysis.xml output_file_1.log output_file_2.log ... tree_file.trees
# Expect at least 3 files
# This matches column names in log files to parameter names in the original XML to set initial conditions

xml_filename = ARGV.shift
tree_filename = ARGV.pop
log_filenames = ARGV

# Go through log files and create a hash of parameter name to value
param = Hash.new
log_filenames.each {|log_filename|

	lines = File.open(log_filename,"r").readlines
	lines.delete_if{|line|
		line[0] == "#"
	}
	
	names = lines[0].split("\t")
	values = lines[-1].split("\t")
		
	names.zip(values).map{|name, value|
		param[name] = value
	}

	
}

# If there is a string of names in the form name1 \t name2 \t name3, this is a parameter array
# and its map should be name to a list of values separated by spaces
additional = Hash.new
param.each_pair{|name, value|
	m = name.match(/^(\S+[^0-9])[0-9]+$/)
	if m != nil
		shortname = m[1]
		if additional[shortname] == nil
			additional[shortname] = "#{value}"
		else
			additional[shortname] += " #{value}"
		end
	end
}
param.merge!(additional)

# Remove non-initialized parameters from param.
empty_parameters = ["treeModel.rootHeight"]
empty_parameters.each {|name|
	param.delete(name)
}

# Go through trees file and construct hash of id to taxa name
trees = File.open(tree_filename, "r").readlines
taxa = Hash.new
trees.each { |line|
	m = line.match(/(\d+) '*([A-Za-z0-9\-\_\.\/\|]+)'*/)
	if m != nil
		id = m[1]
		name = m[2]
		taxa[id] = name
	end
	m = line.match(/tree STATE_/)
	if m != nil
		break
	end
}

# Go through last tree and replace ids with taxa names

tree = trees[-1]
m = tree.match(/tree STATE/)
if m == nil
	tree = trees[-2]
end
tree.gsub!(/\d+\[/) {|s| taxa[s.chop]+"[" }
tree.gsub!(/\d+\:/) {|s| taxa[s.chop]+":" }
tree.sub!(/^tree STATE_.+ = \[\&R\] /, "")

# Go through XML file and replace initial parameter values with values from param
hold = false
File.open(xml_filename,"r").each_line {|line|

	m = line.match(/<coalescentTree id="startingTree">/)
	if m != nil
		hold = true
	end
		
	m = line.match(/parameter id="([^"]+)"/)
	if m != nil
		name = m[1]
		value = param[name]											# check for value in param
		if value != nil
			n = line.match(/value=/)								# check line for value=""
			if n != nil
				line.sub!(/value="([^"]+)"/, "value=\"#{value}\"")
			else
				line.sub!(/parameter id="([^"]+)"/, "parameter id=\"#{name}\" value=\"#{value}\"")
			end
		end
	end
	
	if hold == false
		puts line
	end
	
	m = line.match(/<\/coalescentTree>/)
	if m != nil
		hold = false
		puts "\t<newick id=\"startingTree\">"
		puts "\t\t#{tree}"
		puts "\t<\/newick>"
		puts
	end	
	
}