Class: Bio::Phylip::DistanceMatrix

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/phylip/distance_matrix.rb

Overview

This is a parser class for phylip distance matrix data created by dnadist, protdist, or restdist commands.

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str) ⇒ DistanceMatrix

creates a new distance matrix object



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# File 'lib/bio/appl/phylip/distance_matrix.rb', line 27

def initialize(str)
  data = str.strip.split(/(?:\r\n|\r|\n)/)
  @otus = data.shift.to_s.strip.to_i
  prev = nil
  data.collect! do |x|
    if /\A +/ =~ x and prev then
      prev.concat x.strip.split(/\s+/)
      nil
    else
      prev = x.strip.split(/\s+/)
      prev
    end
  end
  data.compact!
  if data.size != @otus then
    raise "inconsistent data (OTUs=#{@otus} but #{data.size} rows)"
  end
  @otu_names = data.collect { |x| x.shift }
  mat = data.collect do |x|
    if x.size != @otus then
      raise "inconsistent data (OTUs=#{@otus} but #{x.size} columns)"
    end
    x.collect { |y| y.to_f }
  end
  @matrix = Matrix.rows(mat, false)
  @original_matrix = Matrix.rows(data, false)
end

Instance Attribute Details

#matrix ⇒ Object (readonly)

distance matrix (returns Ruby’s Matrix object)



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# File 'lib/bio/appl/phylip/distance_matrix.rb', line 56

def matrix
  @matrix
end

#original_matrix ⇒ Object (readonly)

matrix contains values as original strings. Use it when you doubt precision of floating-point numbers.



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# File 'lib/bio/appl/phylip/distance_matrix.rb', line 60

def original_matrix
  @original_matrix
end

#otu_names ⇒ Object (readonly)

names of OTUs



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# File 'lib/bio/appl/phylip/distance_matrix.rb', line 66

def otu_names
  @otu_names
end

#otus ⇒ Object (readonly)

number of OTUs



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# File 'lib/bio/appl/phylip/distance_matrix.rb', line 63

def otus
  @otus
end

Class Method Details

.generate(matrix, otu_names = nil, options = {}) ⇒ Object

Generates a new phylip distance matrix formatted text as a string.



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# File 'lib/bio/appl/phylip/distance_matrix.rb', line 69

def self.generate(matrix, otu_names = nil, options = {})
  if matrix.row_size != matrix.column_size then
    raise "must be a square matrix"
  end
  otus = matrix.row_size
  names = (0...otus).collect do |i|
    name = ((otu_names and otu_names[i]) or "OTU#{i.to_s}")
    name
  end
  data = (0...otus).collect do |i|
    x = (0...otus).collect { |j|  sprintf("%9.6f", matrix[i, j]) }
    x.unshift(sprintf("%-10s", names[i])[0, 10])

    str = x[0, 7].join(' ') + "\n"
    7.step(otus + 1, 7) do |k|
      str << ' ' + x[k, 7].join(' ') + "\n"
    end
    str
  end
  sprintf("%5d\n", otus) + data.join('')
end