class Bio::Phylip::DistanceMatrix

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

Attributes

matrix[R]

distance matrix (returns Ruby’s Matrix object)

original_matrix[R]

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

otu_names[R]

names of OTUs

otus[R]

number of OTUs

Public Class Methods

generate(matrix, otu_names = nil, options = {}) click to toggle source

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

   # File lib/bio/appl/phylip/distance_matrix.rb
69 def self.generate(matrix, otu_names = nil, options = {})
70   if matrix.row_size != matrix.column_size then
71     raise "must be a square matrix"
72   end
73   otus = matrix.row_size
74   names = (0...otus).collect do |i|
75     name = ((otu_names and otu_names[i]) or "OTU#{i.to_s}")
76     name
77   end
78   data = (0...otus).collect do |i|
79     x = (0...otus).collect { |j|  sprintf("%9.6f", matrix[i, j]) }
80     x.unshift(sprintf("%-10s", names[i])[0, 10])
81 
82     str = x[0, 7].join(' ') + "\n"
83     7.step(otus + 1, 7) do |k|
84       str << ' ' + x[k, 7].join(' ') + "\n"
85     end
86     str
87   end
88   sprintf("%5d\n", otus) + data.join('')
89 end

new(str) click to toggle source

creates a new distance matrix object

   # File lib/bio/appl/phylip/distance_matrix.rb
27 def initialize(str)
28   data = str.strip.split(/(?:\r\n|\r|\n)/)
29   @otus = data.shift.to_s.strip.to_i
30   prev = nil
31   data.collect! do |x|
32     if /\A +/ =~ x and prev then
33       prev.concat x.strip.split(/\s+/)
34       nil
35     else
36       prev = x.strip.split(/\s+/)
37       prev
38     end
39   end
40   data.compact!
41   if data.size != @otus then
42     raise "inconsistent data (OTUs=#{@otus} but #{data.size} rows)"
43   end
44   @otu_names = data.collect { |x| x.shift }
45   mat = data.collect do |x|
46     if x.size != @otus then
47       raise "inconsistent data (OTUs=#{@otus} but #{x.size} columns)"
48     end
49     x.collect { |y| y.to_f }
50   end
51   @matrix = Matrix.rows(mat, false)
52   @original_matrix = Matrix.rows(data, false)
53 end