Class: Bio::EBD::DistanceMatrix

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-express_beta_diversity/distance_matrix.rb

Overview

Distance matrix output from express beta diversity (Donovan Parks et al). Similar to phylip distance format, but not quite the same.

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ DistanceMatrix

Returns a new instance of DistanceMatrix.



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# File 'lib/bio-express_beta_diversity/distance_matrix.rb', line 12

def initialize
  @distance_matrix = []
  @sample_names = []
end

Instance Attribute Details

#distance_matrix ⇒ Object

Returns the value of attribute distance_matrix.



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# File 'lib/bio-express_beta_diversity/distance_matrix.rb', line 9

def distance_matrix
  @distance_matrix
end

#sample_names ⇒ Object

Returns the value of attribute sample_names.



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# File 'lib/bio-express_beta_diversity/distance_matrix.rb', line 10

def sample_names
  @sample_names
end

Class Method Details

.parse_from_file(filename) ⇒ Object 



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# File 'lib/bio-express_beta_diversity/distance_matrix.rb', line 17

def self.parse_from_file(filename)
  ebd = Bio::EBD::DistanceMatrix.new

  line = 1
  expected_number_of_samples = nil
  CSV.foreach(filename, :col_sep => "\t") do |row|
    if line == 1
      # First line is the number of samples
      raise "Parse exception at this row: #{row.inspect}, expected" unless row.length == 1
      expected_number_of_samples = row[0].to_i
    else
      # all other lines are the sample names and then the lower
      # triangular distance matrix
      sample_index = line-2
      raise "Parse exception at this row: #{row.inspect}" unless row.length == sample_index+1
      ebd.sample_names.push row[0]

      distances = row[1...row.length].collect{|d| d.to_f}
      ebd.distance_matrix[sample_index] = distances
    end
    line += 1
  end

  return ebd
end

Instance Method Details

#distance(sample1, sample2) ⇒ Object

Return the floating point distance between a pair of samples



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# File 'lib/bio-express_beta_diversity/distance_matrix.rb', line 48

def distance(sample1, sample2)
  index1 = @sample_names.find_index{|n| n==sample1}
  index2 = @sample_names.find_index{|n| n==sample2}
  raise "error extracting the EBD distance between #{sample1.inspect} and #{sample2.inspect}" unless index1 and index2 and index2 != index1
  if index1 > index2
    return @distance_matrix[index1][index2]
  else
    return @distance_matrix[index2][index1]
  end
end

#number_of_samples ⇒ Object 



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# File 'lib/bio-express_beta_diversity/distance_matrix.rb', line 43

def number_of_samples
  @sample_names.length
end