bio 1.2.1 → 1.3.0

data/lib/bio/sequence.rb

@@ -9,7 +9,7 @@
 #               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 $
+# $Id: sequence.rb,v 0.58.2.12 2008/06/17 15:25:22 ngoto Exp $
 #
 
 require 'bio/sequence/compat'
@@ -70,6 +70,9 @@ class Sequence
   autoload :AA,      'bio/sequence/aa'
   autoload :Generic, 'bio/sequence/generic'
   autoload :Format,  'bio/sequence/format'
+  autoload :Adapter, 'bio/sequence/adapter'
+
+  include Format
 
   # Create a new Bio::Sequence object
   #
@@ -95,71 +98,137 @@ class Sequence
   # 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)
+    begin
+      seq.__send__(sym, *args, &block)
+    rescue NoMethodError => evar
+      lineno = __LINE__ - 2
+      file = __FILE__
+      bt_here = [ "#{file}:#{lineno}:in \`__send__\'",
+                  "#{file}:#{lineno}:in \`method_missing\'"
+                ]
+      if bt_here == evar.backtrace[0, 2] then
+        bt = evar.backtrace[2..-1]
+        evar = evar.class.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
+        evar.set_backtrace(bt)
+      end
+      #p lineno
+      #p file
+      #p bt_here
+      #p evar.backtrace
+      raise(evar)
+    end
   end
   
-  # The sequence identifier.  For example, for a sequence
-  # of Genbank origin, this is the accession number.
+  # The sequence identifier (String).  For example, for a sequence
+  # of Genbank origin, this is the locus name.
+  # For a sequence of EMBL origin, this is the primary accession number.
   attr_accessor :entry_id
   
-  # A String with a description of the sequence
+  # A String with a description of the sequence (String)
   attr_accessor :definition
   
-  # An Array of Bio::Feature objects
+  # Features (An Array of Bio::Feature objects)
   attr_accessor :features
   
-  # An Array of Bio::Reference objects
+  # References (An Array of Bio::Reference objects)
   attr_accessor :references
   
-  # A comment String
+  # Comments (String or an Array of String)
   attr_accessor :comments
   
-  # Date from sequence source. Often date of deposition.
-  attr_accessor :date
-  
-  # An Array of Strings
+  # Keywords (An Array of String)
   attr_accessor :keywords
   
-  # An Array of Strings; links to other database entries.
+  # Links to other database entries.
+  # (An Array of Bio::Sequence::DBLink objects)
   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
+
+  #---
+  # Attributes below have been added during BioHackathon2008
+  #+++
   
-  # 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
+  # Version number of the sequence (String or Integer).
+  # Unlike <tt>entry_version</tt>, <tt>sequence_version</tt> will be changed
+  # when the submitter of the sequence updates the entry.
+  # Normally, the same entry taken from different databases (EMBL, GenBank,
+  # and DDBJ) may have the same sequence_version.
+  attr_accessor :sequence_version
+
+  # Topology (String). "circular", "linear", or nil.
+  attr_accessor :topology
+
+  # Strandedness (String). "single" (single-stranded),
+  # "double" (double-stranded), "mixed" (mixed-stranded), or nil.
+  attr_accessor :strandedness
+
+  # molecular type (String). "DNA" or "RNA" for nucleotide sequence.
+  attr_accessor :molecule_type
+
+  # Data Class defined by EMBL (String)
+  # See http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_1
+  attr_accessor :data_class
+
+  # Taxonomic Division defined by EMBL/GenBank/DDBJ (String)
+  # See http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_2
+  attr_accessor :division
+
+  # Primary accession number (String)
+  attr_accessor :primary_accession
+
+  # Secondary accession numbers (Array of String)
+  attr_accessor :secondary_accessions
+
+  # Created date of the sequence entry (Date, DateTime, Time, or String)
+  attr_accessor :date_created
+
+  # Last modified date of the sequence entry (Date, DateTime, Time, or String)
+  attr_accessor :date_modified
+
+  # Release information when created (String)
+  attr_accessor :release_created
+
+  # Release information when last-modified (String)
+  attr_accessor :release_modified
+
+  # Version of the entry (String or Integer).
+  # Unlike <tt>sequence_version</tt>, <tt>entry_version</tt> is a database
+  # maintainer's internal version number.
+  # The version number will be changed when the database maintainer
+  # modifies the entry.
+  # The same enrty in EMBL, GenBank, and DDBJ may have different
+  # entry_version.
+  attr_accessor :entry_version
+
+  # Organism species (String). For example, "Escherichia coli".
+  attr_accessor :species
+
+  # Organism classification, taxonomic classification of the source organism.
+  # (Array of String)
+  attr_accessor :classification
+  alias taxonomy classification
+
+  # (not well supported) Organelle information (String).
+  attr_accessor :organelle
+
+  # Namespace of the sequence IDs described in entry_id, primary_accession,
+  # and secondary_accessions methods (String).
+  # For example, 'EMBL', 'GenBank', 'DDBJ', 'RefSeq'.
+  attr_accessor :id_namespace
+
+  # Sequence identifiers which are not described in entry_id,
+  # primary_accession,and secondary_accessions methods
+  # (Array of Bio::Sequence::DBLink objects).
+  # For example, NCBI GI number can be stored.
+  # Note that only identifiers of the entry itself should be stored.
+  # For database cross references, <tt>dblinks</tt> should be used.
+  attr_accessor :other_seqids
 
   # 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
@@ -174,9 +243,9 @@ class Sequence
   def auto
     @moltype = guess
     if @moltype == NA
-      @seq = NA.new(@seq)
+      @seq = NA.new(seq)
     else
-      @seq = AA.new(@seq)
+      @seq = AA.new(seq)
     end
   end
 
@@ -236,7 +305,7 @@ class Sequence
   # * (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
+    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'] +
@@ -309,7 +378,7 @@ class Sequence
   # ---
   # *Returns*:: Bio::Sequence::NA
   def na
-    @seq = NA.new(@seq)
+    @seq = NA.new(seq)
     @moltype = NA
   end
 
@@ -330,146 +399,58 @@ class Sequence
   # ---
   # *Returns*:: Bio::Sequence::AA
   def aa
-    @seq = AA.new(@seq)
+    @seq = AA.new(seq)
     @moltype = AA
   end
-  
-end # Sequence
 
+  # Create a new Bio::Sequence object from a formatted string
+  # (GenBank, EMBL, fasta format, etc.)
+  #
+  #   s = Bio::Sequence.input(str)
+  # ---
+  # *Arguments*:
+  # * (required) _str_: string
+  # * (optional) _format_: format specification (class or nil)
+  # *Returns*:: Bio::Sequence object
+  def self.input(str, format = nil)
+    if format then
+      klass = format
+    else
+      klass = Bio::FlatFile::AutoDetect.default.autodetect(str)
+    end
+    obj = klass.new(str)
+    obj.to_biosequence
+  end
 
-end # Bio
+  # alias of Bio::Sequence.input
+  def self.read(str, format = nil)
+    input(str, format)
+  end
 
+  # accession numbers of the sequence
+  #
+  # *Returns*:: Array of String
+  def accessions
+    [ primary_accession, secondary_accessions ].flatten.compact
+  end
+
+  # Normally, users should not call this method directly.
+  # Use Bio::*#to_biosequence (e.g. Bio::GenBank#to_biosequence).
+  #
+  # Creates a new Bio::Sequence object from database data with an
+  # adapter module.
+  def self.adapter(source_data, adapter_module)
+    biosequence = self.new(nil)
+    biosequence.instance_eval {
+      remove_instance_variable(:@seq)
+      @source_data = source_data
+    }
+    biosequence.extend(adapter_module)
+    biosequence
+  end
+
+end # Sequence
 
-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
 
+end # Bio
 

data/lib/bio/sequence/adapter.rb

@@ -0,0 +1,108 @@
+#
+# = bio/sequence/adapter.rb - Bio::Sequence adapter helper module
+#
+# Copyright::   Copyright (C) 2008
+#               Naohisa Goto <ng@bioruby.org>,
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+require 'bio/sequence'
+
+# Internal use only. Normal users should not use this module.
+#
+# Helper methods for defining adapters used when converting data classes to
+# Bio::Sequence class, with pseudo lazy evaluation and pseudo memoization.
+#
+# This module is used by using "extend", not "include".
+# 
+module Bio::Sequence::Adapter
+
+  autoload :GenBank,     'bio/db/genbank/genbank_to_biosequence'
+  autoload :EMBL,        'bio/db/embl/embl_to_biosequence'
+  autoload :FastaFormat, 'bio/db/fasta/fasta_to_biosequence'
+  autoload :BioSQL,      'bio/db/biosql/biosql_to_biosequence'
+
+  private
+
+  # Defines a reader attribute method with psudo lazy evaluation/memoization.
+  #
+  # It defines a method <i>name</i> like attr_reader, but at the first time
+  # when the method <i>name</i> is called, it acts as follows:
+  # When instance variable @<i>name</i> is not defined,
+  # calls <tt>__get__<i>name</i>(@source_data)</tt> and stores the returned
+  # value to @<i>name</i>, and changes its behavior to the same as
+  # <tt>attr_reader </tt><i>:name</i>.
+  # When instance variable @name is already defined,
+  # its behavior is changed to the same as
+  # <tt>attr_reader </tt><i>:name</i>.
+  # When the object is frozen, storing to the instance variable and
+  # changing methods behavior do not occur, and the value of
+  # <tt>__get__<i>name</i>(@source_data)</tt> is returned.
+  # 
+  # Note that it assumes that the source data object is stored in
+  # @source_data instance variable.
+  def attr_reader_lazy(name)
+    #$stderr.puts "attr_reader_lazy :#{name}"
+    varname = "@#{name}".intern
+    methodname = "__get__#{name}".intern
+
+    # module to reset method's behavior to normal attr_reader
+    reset = "Attr_#{name}".intern
+    const_set(reset, Module.new { attr_reader name })
+    reset_module_name = "#{self}::#{reset}"
+
+    # define attr method
+    module_eval <<__END_OF_DEF__
+      def #{name}
+        unless defined? #{varname} then
+          #$stderr.puts "LAZY #{name}: calling #{methodname}"
+          val = #{methodname}(@source_data)
+          #{varname} = val unless frozen?
+        else
+          val = #{varname}
+        end
+        unless frozen? then
+          #$stderr.puts "LAZY #{name}: finalize: attr_reader :#{name}"
+          self.extend(#{reset_module_name})
+        end
+        val
+      end
+__END_OF_DEF__
+  end
+
+  # Defines a Bio::Sequence to Bio::* adapter method with
+  # psudo lazy evaluation and psudo memoization.
+  #
+  # Without block, defines a private method <tt>__get__<i>name</i>(orig)</tt>
+  # which calls <i>source_method</i> for @source_data.
+  #
+  # def__get__(name, source_method) is the same as:
+  #   def __get__name(orig); orig.source_method; end
+  #   attr_reader_lazy name
+  #
+  # If block is given, <tt>__get__<i>name</i>(orig)</tt> is defined
+  # with the block. The @source_data is given as an argument of the block,
+  # i.e. the block must get an argument.
+  #
+  def def_biosequence_adapter(name, source_method = name, &block)
+    methodname = "__get__#{name}".intern
+
+    if block then
+      define_method(methodname, block)
+    else
+      module_eval <<__END_OF_DEF__
+        def #{methodname}(orig)
+          orig.#{source_method}
+        end
+__END_OF_DEF__
+    end
+    private methodname
+    attr_reader_lazy name
+    true
+  end
+
+end #module Bio::Sequence::Adapter
+
+