Module: Dphil::PAUP

Defined in:
lib/dphil/paup.rb

Overview

PAUP* Log Processor

Constant Summary collapse

BRANCH_REGEXP = 
/^Branch lengths and linkages.*?\n\-{40,}\n(.*?)\n\-{40,}\n^Sum.*?(^Tree length =.*?)\n\n/m
CHGLIST_REGEXP = 
/^Character change lists:.*?\n\-{40,}\n(.*?)\n\n/m

Class Method Summary collapse

Class Method Details

.parse_trees(infile) ⇒ Object 



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# File 'lib/dphil/paup.rb', line 8

def self.parse_trees(infile)
  infile = File.expand_path(infile)
  return STDERR.puts("File #{infile} not found.") unless File.exist?(infile)

  data = File.read(infile).to_s.split(/^Tree ([0-9]+)\:$/)
  return data if data.empty?

  hash = { preamble: data.shift.strip }

  trees = {}
  data.each_slice(2) do |k, v|
    next trees[:remainder] = k if v.nil?
    branches = v.match(BRANCH_REGEXP)&.captures
    changes = v.match(CHGLIST_REGEXP)&.captures
    arr = []
    arr.concat(i[lengths stats].zip(branches)) unless branches.nil?
    arr << [:changes, changes[0]] unless branches.nil?
    trees[k.to_i] = arr.to_h
  end

  hash.merge(trees)
end