BioRuby

% sudo gem install bio

% su 
# ruby setup.rb

> gem install bio

#!/usr/bin/env ruby
require 'bio'

# create a DNA sequence object from a String
dna = Bio::Sequence::NA.new("atcggtcggctta")

# create an RNA sequence object from a String
rna = Bio::Sequence::NA.new("auugccuacauaggc")

# create a Protein sequence from a String
aa = Bio::Sequence::AA.new("AGFAVENDSA")
 
# you can check if the sequence contains illegal characters
# that is not an accepted IUB character for that symbol
# (should prepare a Bio::Sequence::AA#illegal_symbols method also)
puts dna.illegal_bases

# translate and concatenate a DNA sequence to Protein sequence
newseq = aa + dna.translate
puts newseq # => "AGFAVENDSAIGRL"

#!/usr/bin/env ruby
 
# you can use Bio::Sequence object as a String object to print, seamlessly
dna = Bio::Sequence::NA.new("atgc")
puts dna        # => "atgc"
str = dna.to_s
puts str        # => "atgc"

#!/usr/bin/env ruby

require 'bio'

# create a DNA sequence
seq = Bio::Sequence::NA.new("atggccattgaatga")
 
# translate to protein
prot = seq.translate
 
# prove that it worked
puts seq   # => "atggccattgaatga"
puts prot  # => "MAIE*"

#!/usr/bin/env ruby
 
require 'bio'
 
# make a 'codon'
codon = Bio::Sequence::NA.new("uug")
 
# you can translate the codon as described in the previous section.
puts codon.translate  # => "L"

#!/usr/bin/env ruby
 
require 'bio'
 
# make a 'codon'
codon = Bio::Sequence::NA.new("uug")
 
# select the standard codon table
codon_table = Bio::CodonTable[1]
 
# You need to convert RNA codon to DNA alphabets because the
# CodonTable in BioRuby is implemented as a static Hash with keys
# expressed in DNA alphabets (not RNA alphabets).
codon2 = codon.dna
 
# get the representation of that codon and translate to amino acid.
amino_acid = codon_table[codon2]
puts amino_acid        # => "L"

#!/usr/bin/env ruby
 
require 'bio'
 
# Generates a sample 100bp sequence.
seq1 = Bio::Sequence::NA.new("aatgacccgt" * 10)
 
# Naming this sequence as "testseq" and print in FASTA format
# (folded by 60 chars per line).
puts seq1.to_fasta("testseq", 60)

#!/usr/bin/env ruby
 
require 'bio'
 
file = Bio::FastaFormat.open(ARGV.shift)
file.each do |entry|
# do something on each fasta sequence entry
end

#!/usr/bin/env ruby
 
require 'bio'
 
Bio::FlatFile.auto(ARGF) do |ff|
ff.each do |entry|
  # do something on each fasta sequence entry
end
end

#!/usr/bin/env ruby
 
require 'bio'
 
Bio::FlatFile.open(Bio::FastaFormat, ARGV[0]) do |ff|
  ff.each do |entry|
    # do something on each fasta sequence entry
  end
end