Class: Bio::Hello

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-hello.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(string = nil) ⇒ Hello

Returns a new instance of Hello.



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# File 'lib/bio-hello.rb', line 72

def initialize(string = nil)
  @message = string || "HELLO*BIORUBY"
  @aa = aaseq(@message)
  @ct = codon_table
end

Instance Attribute Details

#aa ⇒ Object (readonly)

Returns the value of attribute aa.



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# File 'lib/bio-hello.rb', line 70

def aa
  @aa
end

#message ⇒ Object (readonly)

Returns the value of attribute message.



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# File 'lib/bio-hello.rb', line 70

def message
  @message
end

#na ⇒ Object (readonly)

Returns the value of attribute na.



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# File 'lib/bio-hello.rb', line 70

def na
  @na
end

Class Method Details

.decode(string) ⇒ Object 



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# File 'lib/bio-hello.rb', line 138

def self.decode(string)
  self.new.decode(string)
end

.encode(string) ⇒ Object 



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# File 'lib/bio-hello.rb', line 134

def self.encode(string)
  self.new.encode(string)
end

Instance Method Details

#aaseq(string = "") ⇒ Object 



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# File 'lib/bio-hello.rb', line 104

def aaseq(string = "")
  aa = string.upcase.gsub(/[^A-Z]+/, ' ').strip.tr(' ', '*')
  Bio::Sequence::AA.new(aa)
end

#codon_table ⇒ Object

ad hoc modifications to support 26 alphabets (only confirmed with the codon table 1)



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# File 'lib/bio-hello.rb', line 80

def codon_table
  ct = Bio::CodonTable.copy(1)

  # O Pyl pyrrolysine
  ct['tag'] = 'O'

  # U Sec selenocysteine
  ct['tga'] = 'U'

  # B Asx asparagine/aspartic acid [DN]
  ct['nac'] = 'B'  # can be 'uac' (Y) or 'cac' (H) but please omit.
  
  # J Xle isoleucine/leucine [IL]
  ct['ctn'] = 'J'  # should also include 'tt[ag]' (L), 'at[tca]' (I).

  # Z Glx glutamine/glutamic acid [EQ]
  ct['nag'] = 'Z'  # can be 'aag' (K) or 'tag' (*/O) but please omit.

  # X Xaa unknown [A-Z]
  ct['nnn'] = 'X'

  return ct
end

#decode(string = nil) ⇒ Object 



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# File 'lib/bio-hello.rb', line 126

def decode(string = nil)
  if string
    @na = Bio::Sequence::NA.new(string)
  end
  aa = @na.translate(1, @ct)
  @aa = Bio::Sequence::AA.new(aa)
end

#encode(string = nil) ⇒ Object 



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# File 'lib/bio-hello.rb', line 117

def encode(string = nil)
  if string
    @message = string
    @aa = aaseq(string)
  end
  na = @aa.split(//).map{|a| @ct.revtrans(a).first}.join
  @na = Bio::Sequence::NA.new(na)
end

#helix(string = nil) ⇒ Object 



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# File 'lib/bio-hello.rb', line 142

def helix(string = nil)
  if string
    @na = naseq(string)
  end
  dna = @na.clone
  len = @na.length

  if len < 16
    dna += 'n' * (16 - len)
  end

  pairs = [ [5, 0], [4, 2], [3, 3], [2, 4], 
            [1, 4], [0, 3], [0, 2], [1, 0] ]

  count = 0
  dna.window_search(16, 16) do |subseq|
    pairs.each_with_index do |ij, x|
      count += 1
      break if count > len
      base = subseq[x, 1]
      puts ' ' * ij[0] + base + '-' * ij[1] + base.complement
    end
    pairs.reverse.each_with_index do |ij, x|
      count += 1
      break if count > len
      base = subseq[x + 8, 1]
      puts ' ' * ij[0] + base.complement + '-' * ij[1] + base
    end
  end
  return ""
end

#naseq(string) ⇒ Object 



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# File 'lib/bio-hello.rb', line 109

def naseq(string)
  if Bio::Sequence.guess(string) == Bio::Sequence::NA
    dna = Bio::Sequence::NA.new(string)
  else
    dna = encode(string)
  end
end