Class: Bio::AAindex1

Inherits:
AAindex show all
Defined in:
lib/bio/db/aaindex.rb

Overview

Description

Parser class for AAindex1, Amino Acid Index Database.

Examples

# auto-detection of data format by using Bio::AAindex class
aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")

# parse a file and get contents
aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
aax1.entry_id
aax1.index

References

Constant Summary

Constants inherited from AAindex

Bio::AAindex::DELIMITER, Bio::AAindex::RS, Bio::AAindex::TAGSIZE

Instance Method Summary collapse

Methods inherited from AAindex

#author, auto, #comment, #dblinks, #definition, #entry_id, #journal, #title

Methods inherited from DB

#entry_id, #exists?, #fetch, #get, open, #tags

Constructor Details

#initialize(entry) ⇒ AAindex1

Returns a new instance of AAindex1.



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# File 'lib/bio/db/aaindex.rb', line 190

def initialize(entry)
  super(entry)
end

Instance Method Details

#correlation_coefficient ⇒ Object

Returns correlation_coefficient (Hash) in the C line.

cf.) => 0.999, ‘CDEF123456’ => 0.543, …



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# File 'lib/bio/db/aaindex.rb', line 197

def correlation_coefficient
  if @data['correlation_coefficient']
    @data['correlation_coefficient']
  else
    hash = {}
    ary = field_fetch('C').split(' ')
    ary.each do |x|
      next unless x =~ /^[A-Z]/
      hash[x] = ary[ary.index(x) + 1].to_f
    end
    @data['correlation_coefficient'] = hash
  end
end

#index(type = :float) ⇒ Object

Returns the index (Array) in the I line.

an argument: :string, :float, :zscore or :integer



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# File 'lib/bio/db/aaindex.rb', line 214

def index(type = :float)
  aa = %w( A R N D C Q E G H I L K M F P S T W Y V )
  values = field_fetch('I', 1).split(' ')

  if values.size != 20
    raise "Invalid format in #{entry_id} : #{values.inspect}"
  end

  if type == :zscore and values.size > 0
    sum = 0.0
    values.each do |a|
      sum += a.to_f
    end
    mean = sum / values.size # / 20
    var = 0.0
    values.each do |a|
      var += (a.to_f - mean) ** 2
    end
    sd = Math.sqrt(var)
  end

  if type == :integer
    figure = 0
    values.each do |a|
      figure = [ figure, a[/\..*/].length - 1 ].max
    end
  end

  hash = {}

  aa.each_with_index do |a, i|
    case type
    when :string
      hash[a] = values[i]
    when :float
      hash[a] = values[i].to_f
    when :zscore
      hash[a] = (values[i].to_f - mean) / sd
    when :integer
      hash[a] = (values[i].to_f * 10 ** figure).to_i
    end
  end
  return hash
end