Created
July 30, 2012 15:22
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Ruby script to collate nodes and attributes from a BEAST MCC file
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| #!/usr/bin/ruby | |
| # This script reads through an MCC tree and reads out tip attributes | |
| # Converting these to a more parsable tab-deliminated format | |
| # Relies on each label existing for every node | |
| # Load tree from file | |
| filename = ARGV[0] | |
| infile = File.new(filename, "r") | |
| tree = "" | |
| infile.each { |line| | |
| if line=~ /^\s+tree/ | |
| tree = line | |
| end | |
| } | |
| infile.close | |
| # Substitute "|" for "," within label sets | |
| while tree =~ /\{([A-Za-z0-9\-\.\"\|]+),/ | |
| tree.gsub!(/\{([A-Za-z0-9\-\.\"\|]+),/, '{\1|') | |
| end | |
| # Remove "posterior label" | |
| tree.gsub!(/posterior=[0-9\-\.\"\{\}\|]+/, "") | |
| # Replace tiny numbers with 0s | |
| tree.gsub!(/\d+\.\d+E\-\d+/, "0.0") | |
| # collect labels | |
| labels = tree.scan(/[\,\&]([A-Za-z0-9\_\%\.][A-Za-z0-9\_\%\.]+)=/) | |
| labels.flatten!.uniq!.sort! | |
| puts labels.join "\t" | |
| count = labels.length | |
| # Scan tree for labels. Add to label hash and print once hash is full. | |
| h = Hash.new("NA") | |
| tree.scan(/([A-Za-z0-9\_\%\.][A-Za-z0-9\_\%\.]+)=([A-Za-z0-9\-\.\"\{\}\|]+)([\,\]])/) {|label,value,delim| | |
| if delim == "]" | |
| labels.each {|s| | |
| if labels.first == s | |
| print h[s] | |
| elsif labels.last == s | |
| print "\t" + h[s] + "\n" | |
| else | |
| print "\t" + h[s] | |
| end | |
| } | |
| h.clear | |
| end | |
| value.gsub!("|",",") | |
| h[label] = value | |
| } | |
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