Class: Bio::Sequence::AA

Inherits:
String show all
Includes:
Common
Defined in:
lib/bio/sequence/aa.rb,
lib/bio/sequence/compat.rb

Overview

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

Class Method Summary (collapse)

Instance Method Summary (collapse)

Methods included from Common

#+, #<<, #composition, #concat, #normalize!, #randomize, #seq, #splice, #subseq, #to_fasta, #to_s, #total, #window_search

Methods inherited from String

#fill, #fold, #skip, #step, #to_aaseq, #to_naseq

Constructor Details

- (AA) initialize(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:

  • (required) str: String

Returns

Bio::Sequence::AA object



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# File 'lib/bio/sequence/aa.rb', line 58

def initialize(str)
  super
  self.upcase!
  self.tr!(" \t\n\r",'')
end

Class Method Details

+ (Object) 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



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# File 'lib/bio/sequence/compat.rb', line 113

def self.randomize(*arg, &block)
  self.new('').randomize(*arg, &block)
end

Instance Method Details

- (Object) 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



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# File 'lib/bio/sequence/aa.rb', line 95

def codes
  array = []
  self.each_byte do |x|
    array.push(Bio::AminoAcid.names[x.chr])
  end
  return array
end

- (Object) molecular_weight

Estimate molecular weight based on Fasman1976

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

Returns

Float object



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# File 'lib/bio/sequence/aa.rb', line 72

def molecular_weight
  Bio::AminoAcid.weight(self)
end

- (Object) 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



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# File 'lib/bio/sequence/aa.rb', line 112

def names
  self.codes.map do |x|
    Bio::AminoAcid.names[x]
  end
end

- (Object) to_re

Create a ruby regular expression instance (Regexp)

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

Returns

Regexp object



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# File 'lib/bio/sequence/aa.rb', line 83

def to_re
  Bio::AminoAcid.to_re(self)
end