DNA to RNA to Protein

Cervantes · **Posted:** Fri Jan 13, 2006 9:26 pm

This code allows a biology student to take a nucleotide sequence (of DNA), convert it to RNA, then convert that to an amino acid sequence: a protein.

Ruby:

class Array
def each_group( group_length, &block )
self.length.div(group_length).times do |i|
yield self [i * group_length .. (i + 1) * group_length - 1]
end
end

def apply_hash( hsh )
result = self.dup
self.each_with_index do |element, index|
result [index] = hsh [element] if hsh.has_key?( element )
end
result
end
end

class InformationMolecule

attr_reader :sequence

def initialize( sequence )
@sequence = []
if sequence.is_a?( String )
sequence.each_byte do |nt|
@sequence.push( nt.chr.upcase.to_sym )
end
elsif sequence.is_a?( Array )
sequence.each do |nt|
@sequence.push( nt.to_s.upcase.to_sym )
end
end
end

def each_codon( &block )
@sequence.each_group( 3, &block )
end

end

class DNA < InformationMolecule

def initialize( sequence )
super
@@dna2dna = { :A => :T, :T => :A, :C => :G, :G => :C }
@@dna2rna = { :A => :U, :T => :A, :C => :G, :G => :C }
end

def to_rna
RNA.new( @sequence.apply_hash( @@dna2rna ) )
end

def to_cdna
DNA.new( @sequence.apply_hash( @@dna2dna ) )
end

end

class RNA < InformationMolecule

def initialize( sequence )
super
@@rna2dna = { :A => :T, :U => :A, :C => :G, :G => :C }
@@rna2rna = { :A => :U, :U => :A, :C => :G, :G => :C }
@@genetic_code = {
:UUU => :f, :UUC => :f, :UUA => :l, :UUG => :l,
:UCU => :s, :UCC => :s, :UCA => :s, :UCG => :s,
:UAU => :y, :UAC => :y, :UAA => :STOP, :UAG => :STOP,
:UGU => :c, :UGC => :c, :UGA => :STOP, :UGG => :w,
:CUU => :l, :CUC => :l, :CUA => :l, :CUG => :l,
:CCU => :p, :CCC => :p, :CCA => :p, :CCG => :p,
:CAU => :h, :CAC => :h, :CAA => :q, :CAG => :q,
:CGU => :r, :CGC => :r, :CGA => :r, :CGG => :r,
:AUU => :i, :AUC => :i, :AUA => :i, :AUG => :m,
:ACU => :t, :ACC => :t, :ACA => :t, :ACG => :t,
:AAU => :n, :AAC => :n, :AAA => :k, :AAG => :k,
:AGU => :s, :AGC => :s, :AGA => :r, :AGG => :r,
:GUU => :v, :GUC => :v, :GUA => :v, :GUG => :v,
:GCU => :a, :GCC => :a, :GCA => :a, :GCG => :a,
:GAU => :d, :GAC => :d, :GAA => :e, :GAG => :e,
:GGU => :g, :GGC => :g, :GGA => :g, :GGG => :g
}
end

def to_dna
DNA.new( @sequence.apply_hash( @@rna2dna ) )
end

def to_crna
RNA.new( @sequence.apply_hash( @@rna2rna ) )
end

def to_protein
aa_sequence = []
self.each_codon do |codon|
aa = @@genetic_code [codon.join.to_sym]
break if aa == :STOP
aa_sequence.push( aa )
end
Protein.new( aa_sequence )
end

end

class Protein

attr_reader :sequence
attr_reader :full_name_sequence

def initialize( aa_sequence )
@sequence = []
if aa_sequence.is_a?( String )
aa_sequence.each_byte do |aa|
@sequence.push( aa.chr.upcase.to_sym )
end
elsif aa_sequence.is_a?( Array )
aa_sequence.each do |aa|
@sequence.push( aa.to_sym )
end
end
@@aa_code = {
:f => :Phenylalanine,
:l => :Leucine,
:i => :Isoleucine,
:m => :Methionine,
:v => :Valine,
:s => :Serine,
:p => :Proline,
:t => :Threonine,
:a => :Alanine,
:y => :Tyrosine,
:h => :Histidine,
:q => :Glutamine,
:n => :Asparagine,
:k => :Lysine,
:d => :"Aspartic acid",
:e => :"Glutamic acid",
:c => :Cysteine,
:w => :Tryptophan,
:r => :Arginine,
:g => :Glycine
}
@full_name_sequence = @sequence.apply_hash( @@aa_code )
end

end

#nt = ""
#File.open( "nt sequence.txt").each { |line| nt += line.chomp }
#File.open( "aa sequence.txt", "w" ).puts( DNA.new( nt ).to_rna.to_protein.full_name_sequence )

puts DNA.new( "gattacctcggguuu" ).to_rna.to_protein.full_name_sequence

For a bigger nucleotide sequence, try the attached file and switch the commenting at the end of the program.

wtd · **Posted:** Fri Jan 13, 2006 11:29 pm

code:

class Array
def each_group( group_length, &block )
self.length.div(group_length).times do |i|
yield self [i * group_length .. (i + 1) * group_length - 1]
end
end

Why does each_group accept &block? This parameter is not used in the method.

wtd · **Posted:** Fri Jan 13, 2006 11:34 pm

Also, when you have a method that takes a single argument, you can ellide the parentheses. This is often used to great effect when the method ends in a question mark.

Cervantes · **Posted:** Sat Jan 14, 2006 11:09 am

wtd wrote:

code:

class Array
def each_group( group_length, &block )
self.length.div(group_length).times do |i|
yield self [i * group_length .. (i + 1) * group_length - 1]
end
end

Why does each_group accept &block? This parameter is not used in the method.

Thanks for pointing that out. I had thought I needed it as a way to pass the block to each_group from each_codon, but apparently not: I can still call each_group from each_codon with

code:

@sequence.each_group( 3, &block )

Thanks.

Andy · **Posted:** Thu Feb 02, 2006 9:44 am

wow.. believe it or not, that was part of an assignment in cs134 at waterloo.. well the assignment had alot more to it.. but this was definitely in it

wtd · **Posted:** Thu Feb 02, 2006 2:17 pm

wtd wrote:

code:

class Array
def each_group( group_length, &block )
self.length.div(group_length).times do |i|
yield self [i * group_length .. (i + 1) * group_length - 1]
end
end

Why does each_group accept &block? This parameter is not used in the method.

In fact, let's clean that up some more.

code:

def each_group(group_length)
(length / group_length).times do |i|
yield self[i * group_length ... (i + 1) * group_length]
end
end

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