jandot-bio 1.2.1

data/lib/bio/sequence.rb

@@ -0,0 +1,475 @@
+#
+# = bio/sequence.rb - biological sequence class
+#
+# Copyright::   Copyright (C) 2000-2006
+#               Toshiaki Katayama <k@bioruby.org>,
+#               Yoshinori K. Okuji <okuji@enbug.org>,
+#               Naohisa Goto <ng@bioruby.org>,
+#               Ryan Raaum <ryan@raaum.org>,
+#               Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::     The Ruby License
+#
+# $Id: sequence.rb,v 0.58 2007/04/05 23:35:39 trevor Exp $
+#
+
+require 'bio/sequence/compat'
+
+module Bio
+
+# = DESCRIPTION
+# Bio::Sequence objects represent annotated sequences in bioruby.
+# A Bio::Sequence object is a wrapper around the actual sequence, 
+# represented as either a Bio::Sequence::NA or a Bio::Sequence::AA object.
+# For most users, this encapsulation will be completely transparent.
+# Bio::Sequence responds to all methods defined for Bio::Sequence::NA/AA
+# objects using the same arguments and returning the same values (even though 
+# these methods are not documented specifically for Bio::Sequence).
+#
+# = USAGE
+#   # Create a nucleic or amino acid sequence
+#   dna = Bio::Sequence.auto('atgcatgcATGCATGCAAAA')
+#   rna = Bio::Sequence.auto('augcaugcaugcaugcaaaa')
+#   aa = Bio::Sequence.auto('ACDEFGHIKLMNPQRSTVWYU')
+# 
+#   # Print it out
+#   puts dna.to_s
+#   puts aa.to_s
+# 
+#   # Get a subsequence, bioinformatics style (first nucleotide is '1')
+#   puts dna.subseq(2,6)
+# 
+#   # Get a subsequence, informatics style (first nucleotide is '0')
+#   puts dna[2,6]
+# 
+#   # Print in FASTA format
+#   puts dna.output(:fasta)
+# 
+#   # Print all codons
+#   dna.window_search(3,3) do |codon|
+#     puts codon
+#   end
+# 
+#   # Splice or otherwise mangle your sequence
+#   puts dna.splicing("complement(join(1..5,16..20))")
+#   puts rna.splicing("complement(join(1..5,16..20))")
+# 
+#   # Convert a sequence containing ambiguity codes into a 
+#   # regular expression you can use for subsequent searching
+#   puts aa.to_re
+# 
+#   # These should speak for themselves
+#   puts dna.complement
+#   puts dna.composition
+#   puts dna.molecular_weight
+#   puts dna.translate
+#   puts dna.gc_percent
+class Sequence
+
+  autoload :Common,  'bio/sequence/common'
+  autoload :NA,      'bio/sequence/na'
+  autoload :AA,      'bio/sequence/aa'
+  autoload :Generic, 'bio/sequence/generic'
+  autoload :Format,  'bio/sequence/format'
+
+  # Create a new Bio::Sequence object
+  #
+  #   s = Bio::Sequence.new('atgc')
+  #   puts s                                  #=> 'atgc'
+  #
+  # Note that this method does not intialize the contained sequence
+  # as any kind of bioruby object, only as a simple string
+  #
+  #   puts s.seq.class                        #=> String
+  #
+  # See Bio::Sequence#na, Bio::Sequence#aa, and Bio::Sequence#auto 
+  # for methods to transform the basic String of a just created 
+  # Bio::Sequence object to a proper bioruby object
+  # ---
+  # *Arguments*:
+  # * (required) _str_: String or Bio::Sequence::NA/AA object
+  # *Returns*:: Bio::Sequence object
+  def initialize(str)
+    @seq = str
+  end
+
+  # Pass any unknown method calls to the wrapped sequence object.  see
+  # http://www.rubycentral.com/book/ref_c_object.html#Object.method_missing
+  def method_missing(sym, *args, &block) #:nodoc:
+    @seq.send(sym, *args, &block)
+  end
+  
+  # The sequence identifier.  For example, for a sequence
+  # of Genbank origin, this is the accession number.
+  attr_accessor :entry_id
+  
+  # A String with a description of the sequence
+  attr_accessor :definition
+  
+  # An Array of Bio::Feature objects
+  attr_accessor :features
+  
+  # An Array of Bio::Reference objects
+  attr_accessor :references
+  
+  # A comment String
+  attr_accessor :comments
+  
+  # Date from sequence source. Often date of deposition.
+  attr_accessor :date
+  
+  # An Array of Strings
+  attr_accessor :keywords
+  
+  # An Array of Strings; links to other database entries.
+  attr_accessor :dblinks
+  
+  # A taxonomy String
+  attr_accessor :taxonomy
+  
+  # Bio::Sequence::NA/AA
+  attr_accessor :moltype
+  
+  # The sequence object, usually Bio::Sequence::NA/AA, 
+  # but could be a simple String
+  attr_accessor :seq
+  
+  # Using Bio::Sequence::Format, return a String with the Bio::Sequence
+  # object formatted in the given style.
+  #
+  # Formats currently implemented are: 'fasta', 'genbank', and 'embl'
+  #
+  #   s = Bio::Sequence.new('atgc')
+  #   puts s.output(:fasta)                   #=> "> \natgc\n"
+  #
+  # The style argument is given as a Ruby 
+  # Symbol(http://www.ruby-doc.org/core/classes/Symbol.html)
+  # ---
+  # *Arguments*: 
+  # * (required) _style_: :fasta, :genbank, *or* :embl
+  # *Returns*:: String object
+  def output(style)
+    extend Bio::Sequence::Format
+    case style
+    when :fasta
+      format_fasta
+    when :gff
+      format_gff
+    when :genbank
+      format_genbank
+    when :embl
+      format_embl
+    end
+  end
+
+  # Guess the type of sequence, Amino Acid or Nucleic Acid, and create a 
+  # new sequence object (Bio::Sequence::AA or Bio::Sequence::NA) on the basis
+  # of this guess.  This method will change the current Bio::Sequence object.
+  #
+  #   s = Bio::Sequence.new('atgc')
+  #   puts s.seq.class                        #=> String
+  #   s.auto
+  #   puts s.seq.class                        #=> Bio::Sequence::NA
+  # ---
+  # *Returns*:: Bio::Sequence::NA/AA object
+  def auto
+    @moltype = guess
+    if @moltype == NA
+      @seq = NA.new(@seq)
+    else
+      @seq = AA.new(@seq)
+    end
+  end
+
+  # Given a sequence String, guess its type, Amino Acid or Nucleic Acid, and
+  # return a new Bio::Sequence object wrapping a sequence of the guessed type
+  # (either Bio::Sequence::AA or Bio::Sequence::NA)
+  # 
+  #   s = Bio::Sequence.auto('atgc')
+  #   puts s.seq.class                        #=> Bio::Sequence::NA
+  # ---
+  # *Arguments*:
+  # * (required) _str_: String *or* Bio::Sequence::NA/AA object
+  # *Returns*:: Bio::Sequence object
+  def self.auto(str)
+    seq = self.new(str)
+    seq.auto
+    return seq
+  end
+
+  # Guess the class of the current sequence.  Returns the class
+  # (Bio::Sequence::AA or Bio::Sequence::NA) guessed.  In general, used by
+  # developers only, but if you know what you are doing, feel free.
+  # 
+  #   s = Bio::Sequence.new('atgc')
+  #   puts s.guess                            #=> Bio::Sequence::NA
+  #
+  # There are three parameters: `threshold`, `length`, and `index`.  
+  #
+  # The `threshold` value (defaults to 0.9) is the frequency of 
+  # nucleic acid bases [AGCTUagctu] required in the sequence for this method
+  # to produce a Bio::Sequence::NA "guess".  In the default case, if less
+  # than 90% of the bases (after excluding [Nn]) are in the set [AGCTUagctu],
+  # then the guess is Bio::Sequence::AA.
+  # 
+  #   s = Bio::Sequence.new('atgcatgcqq')
+  #   puts s.guess                            #=> Bio::Sequence::AA
+  #   puts s.guess(0.8)                       #=> Bio::Sequence::AA
+  #   puts s.guess(0.7)                       #=> Bio::Sequence::NA
+  #
+  # The `length` value is how much of the total sequence to use in the
+  # guess (default 10000).  If your sequence is very long, you may 
+  # want to use a smaller amount to reduce the computational burden.
+  #
+  #   s = Bio::Sequence.new(A VERY LONG SEQUENCE)
+  #   puts s.guess(0.9, 1000)  # limit the guess to the first 1000 positions
+  #
+  # The `index` value is where to start the guess.  Perhaps you know there
+  # are a lot of gaps at the start...
+  #
+  #   s = Bio::Sequence.new('-----atgcc')
+  #   puts s.guess                            #=> Bio::Sequence::AA
+  #   puts s.guess(0.9,10000,5)               #=> Bio::Sequence::NA
+  # ---
+  # *Arguments*:
+  # * (optional) _threshold_: Float in range 0,1 (default 0.9)
+  # * (optional) _length_: Fixnum (default 10000)
+  # * (optional) _index_: Fixnum (default 1)
+  # *Returns*:: Bio::Sequence::NA/AA
+  def guess(threshold = 0.9, length = 10000, index = 0)
+    str = @seq.to_s[index,length].to_s.extend Bio::Sequence::Common
+    cmp = str.composition
+
+    bases = cmp['A'] + cmp['T'] + cmp['G'] + cmp['C'] + cmp['U'] +
+            cmp['a'] + cmp['t'] + cmp['g'] + cmp['c'] + cmp['u']
+
+    total = str.length - cmp['N'] - cmp['n']
+
+    if bases.to_f / total > threshold
+      return NA
+    else
+      return AA
+    end
+  end 
+
+  # Guess the class of a given sequence.  Returns the class
+  # (Bio::Sequence::AA or Bio::Sequence::NA) guessed.  In general, used by
+  # developers only, but if you know what you are doing, feel free.
+  # 
+  #   puts .guess('atgc')        #=> Bio::Sequence::NA
+  #
+  # There are three optional parameters: `threshold`, `length`, and `index`.  
+  #
+  # The `threshold` value (defaults to 0.9) is the frequency of 
+  # nucleic acid bases [AGCTUagctu] required in the sequence for this method
+  # to produce a Bio::Sequence::NA "guess".  In the default case, if less
+  # than 90% of the bases (after excluding [Nn]) are in the set [AGCTUagctu],
+  # then the guess is Bio::Sequence::AA.
+  # 
+  #   puts Bio::Sequence.guess('atgcatgcqq')      #=> Bio::Sequence::AA
+  #   puts Bio::Sequence.guess('atgcatgcqq', 0.8) #=> Bio::Sequence::AA
+  #   puts Bio::Sequence.guess('atgcatgcqq', 0.7) #=> Bio::Sequence::NA
+  #
+  # The `length` value is how much of the total sequence to use in the
+  # guess (default 10000).  If your sequence is very long, you may 
+  # want to use a smaller amount to reduce the computational burden.
+  #
+  #   # limit the guess to the first 1000 positions
+  #   puts Bio::Sequence.guess('A VERY LONG SEQUENCE', 0.9, 1000)  
+  #
+  # The `index` value is where to start the guess.  Perhaps you know there
+  # are a lot of gaps at the start...
+  #
+  #   puts Bio::Sequence.guess('-----atgcc')             #=> Bio::Sequence::AA
+  #   puts Bio::Sequence.guess('-----atgcc',0.9,10000,5) #=> Bio::Sequence::NA
+  # ---
+  # *Arguments*:
+  # * (required) _str_: String *or* Bio::Sequence::NA/AA object
+  # * (optional) _threshold_: Float in range 0,1 (default 0.9)
+  # * (optional) _length_: Fixnum (default 10000)
+  # * (optional) _index_: Fixnum (default 1)
+  # *Returns*:: Bio::Sequence::NA/AA
+  def self.guess(str, *args)
+    self.new(str).guess(*args)
+  end
+
+  # Transform the sequence wrapped in the current Bio::Sequence object
+  # into a Bio::Sequence::NA object.  This method will change the current
+  # object.  This method does not validate your choice, so be careful!
+  #
+  #   s = Bio::Sequence.new('RRLE')
+  #   puts s.seq.class                        #=> String
+  #   s.na
+  #   puts s.seq.class                        #=> Bio::Sequence::NA !!!
+  #
+  # However, if you know your sequence type, this method may be 
+  # constructively used after initialization,
+  #
+  #   s = Bio::Sequence.new('atgc')
+  #   s.na
+  # ---
+  # *Returns*:: Bio::Sequence::NA
+  def na
+    @seq = NA.new(@seq)
+    @moltype = NA
+  end
+
+  # Transform the sequence wrapped in the current Bio::Sequence object
+  # into a Bio::Sequence::NA object.  This method will change the current
+  # object.  This method does not validate your choice, so be careful!
+  #
+  #   s = Bio::Sequence.new('atgc')
+  #   puts s.seq.class                        #=> String
+  #   s.aa
+  #   puts s.seq.class                        #=> Bio::Sequence::AA !!!
+  #
+  # However, if you know your sequence type, this method may be 
+  # constructively used after initialization,
+  #
+  #   s = Bio::Sequence.new('RRLE')
+  #   s.aa
+  # ---
+  # *Returns*:: Bio::Sequence::AA
+  def aa
+    @seq = AA.new(@seq)
+    @moltype = AA
+  end
+  
+end # Sequence
+
+
+end # Bio
+
+
+if __FILE__ == $0
+
+  puts "== Test Bio::Sequence::NA.new"
+  p Bio::Sequence::NA.new('')
+  p na = Bio::Sequence::NA.new('atgcatgcATGCATGCAAAA')
+  p rna = Bio::Sequence::NA.new('augcaugcaugcaugcaaaa')
+
+  puts "\n== Test Bio::Sequence::AA.new"
+  p Bio::Sequence::AA.new('')
+  p aa = Bio::Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
+
+  puts "\n== Test Bio::Sequence#to_s"
+  p na.to_s
+  p aa.to_s
+
+  puts "\n== Test Bio::Sequence#subseq(2,6)"
+  p na
+  p na.subseq(2,6)
+
+  puts "\n== Test Bio::Sequence#[2,6]"
+  p na
+  p na[2,6]
+
+  puts "\n== Test Bio::Sequence#to_fasta('hoge', 8)"
+  puts na.to_fasta('hoge', 8)
+
+  puts "\n== Test Bio::Sequence#window_search(15)"
+  p na
+  na.window_search(15) {|x| p x}
+
+  puts "\n== Test Bio::Sequence#total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})"
+  p na.total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})
+
+  puts "\n== Test Bio::Sequence#composition"
+  p na
+  p na.composition
+  p rna
+  p rna.composition
+
+  puts "\n== Test Bio::Sequence::NA#splicing('complement(join(1..5,16..20))')"
+  p na
+  p na.splicing("complement(join(1..5,16..20))")
+  p rna
+  p rna.splicing("complement(join(1..5,16..20))")
+
+  puts "\n== Test Bio::Sequence::NA#complement"
+  p na.complement
+  p rna.complement
+  p Bio::Sequence::NA.new('tacgyrkmhdbvswn').complement
+  p Bio::Sequence::NA.new('uacgyrkmhdbvswn').complement
+
+  puts "\n== Test Bio::Sequence::NA#translate"
+  p na
+  p na.translate
+  p rna
+  p rna.translate
+
+  puts "\n== Test Bio::Sequence::NA#gc_percent"
+  p na.gc_percent
+  p rna.gc_percent
+
+  puts "\n== Test Bio::Sequence::NA#illegal_bases"
+  p na.illegal_bases
+  p Bio::Sequence::NA.new('tacgyrkmhdbvswn').illegal_bases
+  p Bio::Sequence::NA.new('abcdefghijklmnopqrstuvwxyz-!%#$@').illegal_bases
+
+  puts "\n== Test Bio::Sequence::NA#molecular_weight"
+  p na
+  p na.molecular_weight
+  p rna
+  p rna.molecular_weight
+
+  puts "\n== Test Bio::Sequence::NA#to_re"
+  p Bio::Sequence::NA.new('atgcrymkdhvbswn')
+  p Bio::Sequence::NA.new('atgcrymkdhvbswn').to_re
+  p Bio::Sequence::NA.new('augcrymkdhvbswn')
+  p Bio::Sequence::NA.new('augcrymkdhvbswn').to_re
+
+  puts "\n== Test Bio::Sequence::NA#names"
+  p na.names
+
+  puts "\n== Test Bio::Sequence::NA#pikachu"
+  p na.pikachu
+
+  puts "\n== Test Bio::Sequence::NA#randomize"
+  print "Orig  : "; p na
+  print "Rand  : "; p na.randomize
+  print "Rand  : "; p na.randomize
+  print "Rand  : "; p na.randomize.randomize
+  print "Block : "; na.randomize do |x| print x end; puts
+
+  print "Orig  : "; p rna
+  print "Rand  : "; p rna.randomize
+  print "Rand  : "; p rna.randomize
+  print "Rand  : "; p rna.randomize.randomize
+  print "Block : "; rna.randomize do |x| print x end; puts
+
+  puts "\n== Test Bio::Sequence::NA.randomize(counts)"
+  print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'t'=>40}
+  print "Rand  : "; p Bio::Sequence::NA.randomize(counts)
+  print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
+  print "Rand  : "; p Bio::Sequence::NA.randomize(counts)
+  print "Block : "; Bio::Sequence::NA.randomize(counts) {|x| print x}; puts
+
+  puts "\n== Test Bio::Sequence::AA#codes"
+  p aa
+  p aa.codes
+
+  puts "\n== Test Bio::Sequence::AA#names"
+  p aa
+  p aa.names
+
+  puts "\n== Test Bio::Sequence::AA#molecular_weight"
+  p aa.subseq(1,20)
+  p aa.subseq(1,20).molecular_weight
+
+  puts "\n== Test Bio::Sequence::AA#randomize"
+  aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
+  s = Bio::Sequence::AA.new(aaseq)
+  print "Orig  : "; p s
+  print "Rand  : "; p s.randomize
+  print "Rand  : "; p s.randomize
+  print "Rand  : "; p s.randomize.randomize
+  print "Block : "; s.randomize {|x| print x}; puts
+
+  puts "\n== Test Bio::Sequence::AA.randomize(counts)"
+  print "Count : "; p counts = s.composition
+  print "Rand  : "; puts Bio::Sequence::AA.randomize(counts)
+  print "Block : "; Bio::Sequence::AA.randomize(counts) {|x| print x}; puts
+
+end
+
+