Class Bio::Sequence::AA
In: lib/bio/sequence/compat.rb
lib/bio/sequence/aa.rb
Parent: Object

DESCRIPTION

Bio::Sequence::AA represents a bare Amino Acid sequence in bioruby.

USAGE

  # Create an Amino Acid sequence.
  aa = Bio::Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')

  # What are the three-letter codes for all the residues?
  puts aa.codes

  # What are the names of all the residues?
  puts aa.names

  # What is the molecular weight of this peptide?
  puts aa.molecular_weight

Methods

codes   molecular_weight   names   new   randomize   to_re  

Included Modules

Bio::Sequence::Common

Public Class methods

new(str)

Generate an amino acid sequence object from a string. 

  s = Bio::Sequence::AA.new("RRLEHTFVFLRNFSLMLLRY")

or maybe (if you have an amino acid sequence in a file) 

  s = Bio::Sequence:AA.new(File.open('aa.txt').read)

Amino Acid sequences are always all uppercase in bioruby 

  s = Bio::Sequence::AA.new("rrLeHtfV")
  puts s                                  #=> "RRLEHTFVF"

Whitespace is stripped from the sequence 

  s = Bio::Sequence::AA.new("RRL\nELA\tRG\r  RL")
  puts s                                  #=> "RRLELARGRL"

Arguments:

Returns:Bio::Sequence::AA object

[Source]

    # File lib/bio/sequence/aa.rb, line 60
60:   def initialize(str)
61:     super
62:     self.upcase!
63:     self.tr!(" \t\n\r",'')
64:   end
randomize(*arg, &block)

Generate a new random sequence with the given frequency of bases. The sequence length is determined by their cumulative sum. (See also Bio::Sequence::Common#randomize which creates a new randomized sequence object using the base composition of an existing sequence instance). 

  counts = {'R'=>1,'L'=>2,'E'=>3,'A'=>4}
  puts Bio::Sequence::AA.randomize(counts)  #=> "AAEAELALRE" (for example)

You may also feed the output of randomize into a block 

  actual_counts = {'R'=>0,'L'=>0,'E'=>0,'A'=>0}
  Bio::Sequence::AA.randomize(counts) {|x| actual_counts[x] += 1}
  actual_counts                     #=> {"A"=>4, "L"=>2, "E"=>3, "R"=>1}

Arguments:

  • (optional) hash: Hash object
Returns:Bio::Sequence::AA object

[Source]

     # File lib/bio/sequence/compat.rb, line 114
114:   def self.randomize(*arg, &block)
115:     self.new('').randomize(*arg, &block)
116:   end

Public Instance methods

codes()

Generate the list of the names of each residue along with the sequence (3 letters code). Codes used in bioruby are found in the Bio::AminoAcid::NAMES hash. 

  s = Bio::Sequence::AA.new("RRLE")
  puts s.codes                        #=> ["Arg", "Arg", "Leu", "Glu"]
Returns:Array object

[Source]

     # File lib/bio/sequence/aa.rb, line 97
 97:   def codes
 98:     array = []
 99:     self.each_byte do |x|
100:       array.push(Bio::AminoAcid.names[x.chr])
101:     end
102:     return array
103:   end
molecular_weight()

Estimate molecular weight based on Fasman1976 

  s = Bio::Sequence::AA.new("RRLE")
  puts s.molecular_weight             #=> 572.655
Returns:Float object

[Source]

    # File lib/bio/sequence/aa.rb, line 74
74:   def molecular_weight
75:     Bio::AminoAcid.weight(self)
76:   end
names()

Generate the list of the names of each residue along with the sequence (full name). Names used in bioruby are found in the Bio::AminoAcid::NAMES hash. 

  s = Bio::Sequence::AA.new("RRLE")
  puts s.names
              #=> ["arginine", "arginine", "leucine", "glutamic acid"]
Returns:Array object

[Source]

     # File lib/bio/sequence/aa.rb, line 114
114:   def names
115:     self.codes.map do |x|
116:       Bio::AminoAcid.names[x]
117:     end
118:   end
to_re()

Create a ruby regular expression instance (Regexp) 

  s = Bio::Sequence::AA.new("RRLE")
  puts s.to_re                        #=> /RRLE/
Returns:Regexp object

[Source]

    # File lib/bio/sequence/aa.rb, line 85
85:   def to_re
86:     Bio::AminoAcid.to_re(self)
87:   end

[Validate]