Module: MiGA::TaxDist

Defined in:
lib/miga/tax_dist.rb

Overview

Methods for taxonomy identification based on AAI/ANI values.

Class Method Summary collapse

Class Method Details

.aai_path(test) ⇒ Object

Absolute path to the :intax or :novel data file (determined by test) for AAI.


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# File 'lib/miga/tax_dist.rb', line 15

def self.aai_path(test)
  test = test.downcase.to_sym
  return nil unless [:intax, :novel].include? test
  File.expand_path("../_data/aai-#{test}.tsv.gz", __FILE__)
end

.aai_pvalues(aai, test) ⇒ Object

Returns a Hash, where the keys correspond to the taxonomic level (see MiGA::Taxonomy.LONG_RANKS for the meanings), and the values correspond to the p-values of being :intax or :novel, as determined by test.


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# File 'lib/miga/tax_dist.rb', line 24

def self.aai_pvalues(aai, test)
  Zlib::GzipReader.open(aai_path(test)) do |fh|
    keys = nil
    fh.each_line do |ln|
      row = ln.chomp.split /\t/
      if fh.lineno==1
        keys = row[1, row.size-1].map{ |i| i.to_i }
      elsif row.shift.to_f >= aai
        vals = {}
        keys.each do |i|
          v = row.shift
          next if v=="NA"
          rank = i==0 ? :root : MiGA::Taxonomy.KNOWN_RANKS[i-1]
          vals[rank] = v.to_f
        end
        return vals
      end
    end # each_line ln
  end # open fh
  {}
end

.aai_taxtest(aai, test) ⇒ Object

Determines the degree to which a Float aai value indicates similar taxonomy (with test :intax) or a novel taxon (with test :novel). Returns a Hash with “likelihood” phrases as keys and values as an array with cannonical rank (as in MiGA::Taxonomy) and estimated p-value.


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# File 'lib/miga/tax_dist.rb', line 50

def self.aai_taxtest(aai, test)
  meaning = {most_likely:[0,0.01],probably:[0.01,0.1],possibly_even:[0.1,0.5]}
  pv = aai_pvalues(aai, test)
  out = {}
  meaning.each do |phrase, thresholds|
    lwr, upr = thresholds
    min = pv.values.select{ |v| v < upr }.max
    return out if min.nil?
    if min >= lwr
      v = pv.select{ |_,v| v==min }
      out[phrase] = (test==:intax ? v.reverse_each : v).first
    end
  end
  out
end