bio 0.7.0

data/lib/bio/data/na.rb

@@ -0,0 +1,226 @@
+#
+# = bio/data/na.rb - Nucleic Acids
+#
+# Copyright::	Copyright (C) 2001, 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: na.rb,v 0.19 2005/12/10 18:14:22 k Exp $
+#
+# == Synopsis
+#
+# Bio::NucleicAcid class contains data related to nucleic acids.
+#
+# == Usage
+#
+# Examples:
+#
+#   require 'bio'
+#
+#   puts "### na = Bio::NucleicAcid.new"
+#   na = Bio::NucleicAcid.new
+#
+#   puts "# na.to_re('yrwskmbdhvnatgc')"
+#   p na.to_re('yrwskmbdhvnatgc')
+#
+#   puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
+#   p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')
+#
+#   puts "# na.weight('A')"
+#   p na.weight('A')
+#
+#   puts "# Bio::NucleicAcid.weight('A')"
+#   p Bio::NucleicAcid.weight('A')
+#
+#   puts "# na.weight('atgc')"
+#   p na.weight('atgc')
+#
+#   puts "# Bio::NucleicAcid.weight('atgc')"
+#   p Bio::NucleicAcid.weight('atgc')
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio
+
+class NucleicAcid
+
+  module Data
+
+    # IUPAC code
+    # * Faisst and Meyer (Nucleic Acids Res. 20:3-26, 1992)
+    # * http://www.ncbi.nlm.nih.gov/collab/FT/
+
+    NAMES = {
+
+      'y'	=> '[tc]',
+      'r'	=> '[ag]',
+      'w'	=> '[at]',
+      's'	=> '[gc]',
+      'k'	=> '[tg]',
+      'm'	=> '[ac]',
+
+      'b'	=> '[tgc]',
+      'd'	=> '[atg]',
+      'h'	=> '[atc]',
+      'v'	=> '[agc]',
+
+      'n'	=> '[atgc]',
+
+      'a'	=> 'a',
+      't'	=> 't',
+      'g'	=> 'g',
+      'c'	=> 'c',
+      'u'	=> 'u',
+
+      'A'	=> 'Adenine',
+      'T'	=> 'Thymine',
+      'G'	=> 'Guanine',
+      'C'	=> 'Cytosine',
+      'U'	=> 'Uracil',
+
+      'Y'	=> 'pYrimidine',
+      'R'	=> 'puRine',
+      'W'	=> 'Weak',
+      'S'	=> 'Strong',
+      'K'	=> 'Keto',
+      'M'	=> 'aroMatic',
+
+      'B'	=> 'not A',
+      'D'	=> 'not C',
+      'H'	=> 'not G',
+      'V'	=> 'not T',
+    }
+
+    WEIGHT = {
+
+      # Calculated by BioPerl's Bio::Tools::SeqStats.pm :-)
+
+      'a'	=> 135.15,
+      't'	=> 126.13,
+      'g'	=> 151.15,
+      'c'	=> 111.12,
+      'u'	=> 112.10,
+
+      :adenine	=> 135.15,
+      :thymine	=> 126.13,
+      :guanine	=> 151.15,
+      :cytosine	=> 111.12,
+      :uracil	=> 112.10,
+
+      :deoxyribose_phosphate	=> 196.11,
+      :ribose_phosphate		=> 212.11,
+
+      :hydrogen	=> 1.00794,
+      :water	=> 18.015,
+
+    }
+
+    def weight(x = nil, rna = nil)
+      if x
+        if x.length > 1
+          if rna
+            phosphate = WEIGHT[:ribose_phosphate]
+          else
+            phosphate = WEIGHT[:deoxyribose_phosphate]
+          end
+          hydrogen    = WEIGHT[:hydrogen]
+          water       = WEIGHT[:water]
+
+          total = 0.0
+          x.each_byte do |byte|
+            base = byte.chr.downcase
+            if WEIGHT[base]
+              total += WEIGHT[base] + phosphate - hydrogen * 2
+            else
+              raise "Error: invalid nucleic acid '#{base}'"
+            end
+          end
+          total -= water * (x.length - 1)
+        else
+          WEIGHT[x.to_s.downcase]
+        end
+      else
+        WEIGHT
+      end
+    end
+
+    def [](x)
+      NAMES[x]
+    end
+
+    # backward compatibility
+    def names
+      NAMES
+    end
+    alias na names
+
+    def name(x)
+      NAMES[x.to_s.upcase]
+    end
+
+    def to_re(seq, rna = false)
+      str = seq.to_s
+      str.gsub!(/[^atgcu]/) { |base|
+        NAMES[base] || '.'
+      }
+      if rna
+        str.tr!("t", "u")
+      end
+      Regexp.new(str)
+    end
+
+  end
+
+
+  # as instance methods
+  include Data
+
+  # as class methods
+  extend Data
+
+end
+
+end # module Bio
+
+
+if __FILE__ == $0
+
+  puts "### na = Bio::NucleicAcid.new"
+  na = Bio::NucleicAcid.new
+
+  puts "# na.to_re('yrwskmbdhvnatgc')"
+  p na.to_re('yrwskmbdhvnatgc')
+
+  puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
+  p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')
+
+  puts "# na.weight('A')"
+  p na.weight('A')
+
+  puts "# Bio::NucleicAcid.weight('A')"
+  p Bio::NucleicAcid.weight('A')
+
+  puts "# na.weight('atgc')"
+  p na.weight('atgc')
+
+  puts "# Bio::NucleicAcid.weight('atgc')"
+  p Bio::NucleicAcid.weight('atgc')
+
+end

data/lib/bio/db.rb

@@ -0,0 +1,340 @@
+#
+# = bio/db.rb - common API for database parsers
+#
+# Copyright::	Copyright (C) 2001, 2002, 2005
+#		KATAYAMA Toshiaki <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: db.rb,v 0.31 2005/12/07 11:23:51 k Exp $
+#
+# == On-demand parsing and cache
+#
+# The flatfile parsers (sub classes of the Bio::DB) split the original entry
+# into a Hash and store the hash in the @orig instance variable.  To parse
+# in detail is delayed until the method is called which requires a further
+# parsing of a content of the @orig hash.  Fully parsed data is cached in the
+# another hash, @data, separately.
+#
+# == Guide lines for the developers to create an new database class
+#
+# --- Bio::DB.new(entry)
+#
+# The 'new' method should accept the entire entry in one String and
+# return the parsed database object.
+#
+# --- Bio::DB#entry_id
+#
+# Database classes should implement the following methods if appropriate:
+#
+# * entry_id
+# * definition
+#
+# Every sub class should define the following constants if appropriate:
+#
+# * DELIMITER (RS)
+#   * entry separator of the flatfile of the database.
+#   * RS (= record separator) is an alias for the DELIMITER in short.
+#
+# * TAGSIZE
+#   * length of the tag field in the FORTRAN-like format.
+#
+#       |<- tag       ->||<- data                           ---->|
+#       ENTRY_ID         A12345
+#       DEFINITION       Hoge gene of the Pokemonia pikachuae
+#
+# === Template of the sub class
+# 
+#   module Bio
+#   class Hoge < DB
+# 
+#     DELIMITER	= RS = "\n//\n"
+#     TAGSIZE		= 12		# You can omit this line if not needed
+# 
+#     def initialize(entry)
+#     end
+# 
+#     def entry_id
+#     end
+# 
+#   end # class Hoge
+#   end # module Bio
+# 
+# === Recommended method names for sub classes
+# 
+# In general, the method name should be in the singular form when returns
+# a Object (including the case when the Object is a String), and should be
+# the plural form when returns same Objects in Array.  It depends on the
+# database classes that which form of the method name can be use.
+# 
+# For example, GenBank has several REFERENCE fields in one entry, so define
+# Bio::GenBank#references and this method should return an Array of the
+# Reference objects.  On the other hand, MEDLINE has one REFERENCE information
+# per one entry, so define Bio::MEDLINE#reference method and this should
+# return a Reference object.
+# 
+# The method names used in the sub classes should be taken from the following
+# list if appropriate:
+# 
+# --- entry_id #=> String
+# 
+# The entry identifier.
+# 
+# --- definition #=> String
+# 
+# The description of the entry.
+# 
+# --- reference	#=> Bio::Reference
+# --- references #=> Array of Bio::Reference
+# 
+# The reference field(s) of the entry.
+# 
+# --- dblink #=> String
+# --- dblinks #=> Array of String
+# 
+# The link(s) to the other database entry.
+# 
+# --- naseq #=> Bio::Sequence::NA
+# 
+# The DNA/RNA sequence of the entry.
+# 
+# --- nalen #=> Integer
+# 
+# The length of the DNA/RNA sequence of the entry.
+# 
+# --- aaseq #=> Bio::Sequence::AA
+# 
+# The amino acid sequence of the entry.
+# 
+# --- aalen #=> Integer
+# 
+# The length of the amino acid sequence of the entry.
+# 
+# --- seq #=> Bio::Sequence::NA or Bio::Sequence::AA
+# 
+# Returns an appropriate sequence object.
+# 
+# --- position #=> String
+# 
+# The position of the sequence in the entry or in the genome (depends on
+# the database).
+# 
+# --- locations #=> Bio::Locations
+# 
+# Returns Bio::Locations.new(position).
+# 
+# --- division #=> String
+# 
+# The sub division name of the database.
+# 
+# * Example:
+#   * EST, VRL etc. for GenBank
+#   * PATTERN, RULE etc. for PROSITE
+# 
+# --- date #=> String
+# 
+# The date of the entry.
+# Should we use Date (by ParseDate) instead of String?
+# 
+# --- gene #=> String
+# --- genes #=> Array of String
+# 
+# The name(s) of the gene.
+# 
+# --- organism #=> String
+# 
+# The name of the organism.
+# 
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+require 'bio/sequence'
+require 'bio/reference'
+require 'bio/feature'
+
+module Bio
+  
+class DB
+
+  def self.open(filename, *mode, &block)
+    Bio::FlatFile.open(self, filename, *mode, &block)
+  end
+
+  # Returns an entry identifier as a String.  This method must be
+  # implemented in every database classes by overriding this method.
+  def entry_id
+    raise NotImplementedError
+  end
+
+  # Returns a list of the top level tags of the entry as an Array of String.
+  def tags
+    @orig.keys
+  end
+
+  # Returns true or false - wether the entry contains the field of the
+  # given tag name.
+  def exists?(tag)
+    @orig.include?(tag)
+  end
+
+  # Returns an intact field of the tag as a String.
+  def get(tag)
+    @orig[tag]
+  end
+
+  # Similar to the get method, however, fetch returns the content of the
+  # field without its tag and any extra white spaces stripped.
+  def fetch(tag, skip = 0)
+    field = @orig[tag].split(/\n/, skip + 1).last.to_s
+    truncate(field.gsub(/^.{0,#{@tagsize}}/,''))
+  end
+
+
+  private
+
+  # Returns a String with successive white spaces are replaced by one
+  # space and stripeed.
+  def truncate(str)
+    if str
+      str.gsub(/\s+/, ' ').strip
+    else
+      ""
+    end
+  end
+
+  # Returns a tag name of the field as a String.
+  def tag_get(str)
+    if str
+      str[0,@tagsize].strip
+    else
+      ""
+    end
+  end
+
+  # Returns a String of the field without a tag name.
+  def tag_cut(str)
+    if str
+      str[0,@tagsize] = ''
+    else
+      ""
+    end
+  end
+
+  # Returns the content of the field as a String like the fetch method.
+  # Furthermore, field_fetch stores the result in the @data hash.
+  def field_fetch(tag, skip = 0)
+    unless @data[tag]
+      @data[tag] = fetch(tag, skip)
+    end
+    return @data[tag]
+  end
+
+  # Returns an Array containing each line of the field without a tag.
+  # lines_fetch also stores the result in the @data hash.
+  def lines_fetch(tag) 
+    unless @data[tag]  
+      @data[tag] = get(tag).split(/\n/).map{ |l| tag_cut(l) }  
+    end  
+    @data[tag]  
+  end 
+
+end # class DB
+
+
+# Stores a NCBI style (GenBank, KEGG etc.) entry.
+class NCBIDB < DB
+
+  autoload :Common, 'bio/db/genbank/common'
+
+  # The entire entry is passed as a String.  The length of the tag field is
+  # passed as an Integer.  Parses the entry roughly by the entry2hash method
+  # and returns a database object.
+  def initialize(entry, tagsize)
+    @tagsize = tagsize
+    @orig = entry2hash(entry.strip)	# Hash of the original entry
+    @data = {}				# Hash of the parsed entry
+  end
+
+  private
+
+  # Splits an entry into an Array of Strings at the level of top tags.
+  def toptag2array(str)
+    sep = "\001"
+    str.gsub(/\n([A-Za-z\/])/, "\n#{sep}\\1").split(sep)
+  end
+
+  # Splits a field into an Array of Strings at the level of sub tags.
+  def subtag2array(str)
+    sep = "\001"
+    str.gsub(/\n(\s{1,#{@tagsize-1}}\S)/, "\n#{sep}\\1").split(sep)
+  end
+
+  # Returns the contents of the entry as a Hash with the top level tags as
+  # its keys.
+  def entry2hash(entry)
+    hash = Hash.new('')
+
+    fields = toptag2array(entry)
+
+    fields.each do |field|
+      tag = tag_get(field)
+      hash[tag] += field
+    end
+    return hash
+  end
+
+end # class NCBIDB
+
+
+# Class for KEGG databases. Inherits a NCBIDB class.
+class KEGGDB < NCBIDB
+end
+
+
+# Stores an EMBL style (EMBL, TrEMBL, Swiss-Prot etc.) entry.
+class EMBLDB < DB
+
+  autoload :Common, 'bio/db/embl/common'
+
+  # The entire entry is passed as a String.  The length of the tag field is
+  # passed as an Integer.  Parses the entry roughly by the entry2hash method
+  # and returns a database object.
+  def initialize(entry, tagsize)
+    @tagsize = tagsize
+    @orig = entry2hash(entry.strip)	# Hash of the original entry
+    @data = {}			# Hash of the parsed entry
+  end
+
+  private
+
+  # Returns the contents of the entry as a Hash.
+  def entry2hash(entry)
+    hash = Hash.new('')
+    entry.each_line do |line|
+      tag = tag_get(line)
+      next if tag == 'XX'
+      tag = 'R' if tag =~ /^R./	# Reference lines
+      hash[tag] += line
+    end
+    return hash
+  end
+
+end # class EMBLDB
+
+end # module Bio
+