bio 0.7.0

data/lib/bio/db/genbank/genpept.rb

@@ -0,0 +1,73 @@
+#
+# bio/db/genbank/genpept.rb - GenPept database class
+#
+#   Copyright (C) 2002-2004 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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
+#
+#  $Id: genpept.rb,v 1.10 2005/10/23 07:20:37 k Exp $
+#
+
+require 'bio/db/genbank/common'
+require 'bio/db/genbank/genbank'
+
+module Bio
+class GenPept < NCBIDB
+
+  include Bio::NCBIDB::Common
+
+  # LOCUS
+  class Locus
+    def initialize(locus_line)
+      @entry_id = locus_line[12..27].strip
+      @length   = locus_line[29..39].to_i
+      @circular = locus_line[55..62].strip	# always linear
+      @division = locus_line[63..66].strip
+      @date     = locus_line[68..78].strip
+    end
+    attr_accessor :entry_id, :length, :circular, :division, :date
+  end
+
+  def locus
+    @data['LOCUS'] ||= Locus.new(get('LOCUS'))
+  end
+  def entry_id;		locus.entry_id;		end
+  def length;		locus.length;		end
+  def circular;		locus.circular;		end
+  def division;		locus.division;		end
+  def date;		locus.date;		end
+
+
+  # ORIGIN
+  def seq
+    unless @data['SEQUENCE']
+      origin
+    end
+    Bio::Sequence::AA.new(@data['SEQUENCE'])
+  end
+  alias aaseq seq
+  alias aalen length
+
+  def seq_len
+    seq.length
+  end
+
+  # DBSOURCE
+  def dbsource
+    get('DBSOURCE')
+  end
+
+end # GenPept
+end # Bio

data/lib/bio/db/genbank/refseq.rb

@@ -0,0 +1,31 @@
+#
+# bio/db/genbank/refseq.rb - RefSeq database class
+#
+#   Copyright (C) 2000-2004 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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
+#
+#  $Id: refseq.rb,v 1.6 2004/08/23 23:40:35 k Exp $
+#
+
+require 'bio/db/genbank/genbank'
+
+module Bio
+
+class RefSeq < GenBank
+  # Nothing to do (RefSeq database format is completely same as GenBank)
+end
+
+end # Bio

data/lib/bio/db/gff.rb

@@ -0,0 +1,106 @@
+#
+# = bio/db/gff.rb - GFF format class
+#
+# Copyright::  Copyright (C) 2003, 2005
+#              Toshiaki Katayama <k@bioruby.org>
+# License::    LGPL
+#
+# $Id: gff.rb,v 1.5 2005/12/18 15:58:41 k Exp $
+#
+# == Description
+#
+#
+# == Example
+#
+#
+# == References
+#
+# * http://www.sanger.ac.uk/Software/formats/GFF/
+#
+#--
+#
+#  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 GFF
+
+  attr_accessor :records
+
+  def initialize(str = '')
+    @records = Array.new
+    str.each_line do |line|
+      @records << Record.new(line)
+    end
+  end
+
+  class Record
+
+    attr_accessor :seqname
+    attr_accessor :source
+    attr_accessor :feature
+    attr_accessor :start
+    attr_accessor :end
+    attr_accessor :score
+    attr_accessor :strand
+    attr_accessor :frame
+    attr_accessor :attributes
+    attr_accessor :comments
+
+    def initialize(str)
+      @comments = str.chomp[/#.*/]
+      return if /^#/.match(str)
+      @seqname, @source, @feature, @start, @end, @score, @strand, @frame,
+        attributes, = str.chomp.split("\t")
+      @attributes = parse_attributes(attributes) if attributes
+    end
+
+    private
+
+    def parse_attributes(attributes)
+      hash = Hash.new
+      attributes.split(/[^\\];/).each do |atr|
+        key, value = atr.split(' ', 2)
+        hash[key] = value
+      end
+      return hash
+    end
+  end
+
+  class GFF2 < GFF
+    VERSION = 2
+  end
+
+  class GFF3 < GFF
+    VERSION = 3
+  end
+
+end # class GFF
+
+end # module Bio
+
+
+if __FILE__ == $0
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  p Bio::GFF.new(ARGF.read)
+end

data/lib/bio/db/go.rb

@@ -0,0 +1,497 @@
+#
+# = bio/db/go.rb - Classes for Gene Ontology
+#
+# Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
+# License::
+#
+#  $Id: go.rb,v 1.9 2005/10/31 18:32:36 nakao Exp $
+#
+# == Gene Ontology
+#
+# == Example
+#
+# == References
+#--
+#
+#  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/pathway'
+
+module Bio
+
+# = Bio::GO
+# Classes for Gene Ontology http://www.geneontology.org
+class GO
+
+  # = Bio::GO::Ontology
+  #
+  # Container class for ontologies in the DAG Edit format.
+  #
+  # == Example
+  #
+  #  c_data = File.open('component.oontology').read
+  #  go_c = Bio::GO::Ontology.new(c_data)
+  #  p go_c.bfs_shortest_path('0003673','0005632')
+  class Ontology < Bio::Pathway
+
+    # Bio::GO::Ontology.parse_ogids(line)
+    #
+    # Parsing GOID line in the DAGEdit format  
+    #  GO:ID[ ; GO:ID...]
+    def self.parse_goids(line)
+      goids = []
+      loop {
+        if /^ *[$%<]\S.+?;/ =~ line
+          endpoint = line.index(';') + 1
+          line = line[endpoint..line.size]
+        elsif /^,* GO:(\d{7}),*/ =~ line
+          goids << $1.clone
+          endpoint = line.index(goids.last) + goids.last.size
+          line = line[endpoint..line.size]
+        else
+          break
+        end
+      }
+      return goids
+    end
+
+    # Returns a Hash instance of the header lines in ontology flatfile.
+    attr_reader :header_lines
+
+    # 
+    attr_reader :id2term
+
+    #
+    attr_reader :id2id
+
+
+    # Bio::GO::Ontology.new(str)
+    # The DAG Edit format ontology data parser.
+    def initialize(str)
+      @id2term      = {}
+      @header_lines = {}
+      @id2id        = {}
+      adj_list = dag_edit_format_parser(str)
+      super(adj_list)
+    end
+
+        
+    # Returns a GO_Term correspondig with the given GO_ID.
+    def goid2term(goid)
+      term = id2term[goid]
+      term = id2term[id2id[goid]] if term == nil
+      return term
+    end
+
+    private
+
+    # constructing adjaency list for the given ontology
+    def dag_edit_format_parser(str)
+      stack    = []
+      adj_list = []
+      
+      str.each {|line|
+        if /^!(.+?):\s+(\S.+)$/ =~ line  # Parsing head lines
+          tag   = $1
+          value = $2
+          tag.gsub!(/-/,'_')
+          next if tag == 'type'
+          instance_eval("@header_lines['#{tag}'] = '#{value}'")
+          next
+        end
+        
+        case line
+        when /^( *)([$<%])(.+?) ; GO:(\d{7})(\n*)/ # GO Term ; GO:ID
+          depth = $1.length.to_i
+          rel   = $2
+          term  = $3
+          goid1 = goid = $4
+          en    = $5
+          goids = parse_goids(line)   # GO:ID[ ; GO:ID...]
+          synonyms = parse_synonyms(line)  # synonym:Term[ ; synonym:Term...]
+          stack[depth]   = goids.first
+          @id2term[goid] = term
+          
+          next if depth == 0
+
+          goids.each {|goid|
+            @id2term[goid] = term
+            @id2id[goid]   = goids.first
+            adj_list << Bio::Relation.new(stack[depth - 1], goid, rel)
+          }
+            
+          if en == ""
+            loop {
+              case line
+              when /^\n$/
+                break
+              when /^ *([<%]) (.+?) ; GO:(\d{7})/ # <%GO Term ; GO:ID
+                rel1  = $1
+                term1 = $2
+                goid1 = $3
+                goids1 = parse_goids(line)
+                synonyms1 = parse_synonyms(line)
+                
+                @id2term[goid1] = term1
+                goids.each {|goid|
+                  adj_list << Bio::Relation.new(goid1, goid, rel1)
+                }
+              else
+                break
+              end
+            }
+          end
+        end
+      }
+      return adj_list
+    end
+
+
+    # Returns an ary of GO IDs by parsing an entry line in the DAG Edit 
+    # format.
+    def parse_goids(line)
+      Ontology.parse_goids(line)
+    end
+
+    # Bio::GO::Ontology#parse_synonyms(line)
+    def parse_synonyms(line)
+      synonyms = []
+      loop {
+        if / ; synonym:(\S.+?) *[;<%\n]/ =~ line
+          synonyms << $1.clone
+          endpoint = line.index(synonyms.last) + synonyms.last.size
+          line = line[endpoint..line.size]
+        else
+          break
+        end
+      }
+      return synonyms
+    end
+
+  end # class Ontology
+
+
+
+  # = Bio::GO::GeneAssociation
+  # $CVSROOT/go/gene-associations/gene_association.*
+  #
+  # Data parser for the gene_association go annotation.
+  # See also the file format http://www.geneontology.org/doc/GO.annotation.html#file
+  #
+  # == Example
+  #
+  #  mgi_data = File.open('gene_association.mgi').read
+  #  mgi = Bio::GO::GeneAssociation.parser(mgi_data)
+  #
+  #  Bio::GO::GeneAssociation.parser(mgi_data) do |entry|
+  #    p [entry.entry_id, entry.evidence, entry.goid]
+  #  end
+  #
+  class GeneAssociation # < Bio::DB
+
+    # Delimiter
+    DELIMITER = "\n"
+
+    # Delimiter
+    RS = DELIMITER 
+
+    # Retruns an Array of parsed gene_association flatfile.
+    # Block is acceptable.  
+    def self.parser(str)
+      if block_given?
+        str.each(DELIMITER) {|line|
+          next if /^!/ =~ line
+          yield GeneAssociation.new(line)
+        }
+      else
+        galist = []
+        str.each(DELIMITER) {|line|
+          next if /^!/ =~ line
+          galist << GeneAssociation.new(line)
+        }
+        return galist
+      end
+    end
+
+    # Returns DB variable.
+    attr_reader :db                # -> aStr
+
+    # Returns Db_Object_Id variable. Alias to entry_id.
+    attr_reader :db_object_id      # -> aStr
+
+    # Returns Db_Object_Symbol variable.
+    attr_reader :db_object_symbol
+
+    # Returns Db_Object_Name variable.
+    attr_reader :qualifier
+    
+    # Returns Db_Reference variable.
+    attr_reader :db_reference      # -> []
+
+    # Retruns Evidence code variable.
+    attr_reader :evidence
+
+    # Returns the entry is associated with this value.
+    attr_reader :with              # -> []
+
+    # Returns Aspect valiable.
+    attr_reader :aspect
+
+    #
+    attr_reader :db_object_name
+
+    #
+    attr_reader :db_object_synonym # -> []
+
+    # Returns Db_Object_Type variable.
+    attr_reader :db_object_type
+
+    # Returns Taxon variable.
+    attr_reader :taxon
+
+    # Returns Date variable.
+    attr_reader :date
+    
+    # 
+    attr_reader :assigned_by 
+    
+    alias entry_id db_object_id
+
+
+    # Parsing an entry (in a line) in the gene_association flatfile.  
+    def initialize(entry) 
+      tmp = entry.chomp.split(/\t/)
+      @db                = tmp[0] 
+      @db_object_id      = tmp[1]
+      @db_object_symbol  = tmp[2]
+      @qualifier         = tmp[3]  # 
+      @goid              = tmp[4]
+      @db_reference      = tmp[5].split(/\|/)  #
+      @evidence          = tmp[6]
+      @with              = tmp[7].split(/\|/)  # 
+      @aspect            = tmp[8]
+      @db_object_name    = tmp[9]  #
+      @db_object_synonym = tmp[10].split(/\|/) #
+      @db_object_type    = tmp[11]
+      @taxon             = tmp[12] # taxon:4932
+      @date              = tmp[13] # 20010118
+      @assigned_by       = tmp[14] 
+    end
+
+
+    # Returns GO_ID in /\d{7}/ format. Giving not nil arg, returns 
+    # /GO:\d{7}/ style.
+    #
+    # * Bio::GO::GeneAssociation#goid -> "001234"
+    # * Bio::GO::GeneAssociation#goid(true) -> "GO:001234"
+    def goid(org = nil)
+      if org
+        @goid
+      else
+        @goid.sub('GO:','')
+      end
+    end
+
+    # Bio::GO::GeneAssociation#to_str -> a line of gene_association file.
+    def to_str
+      return [@db, @db_object_id, @db_object_symbol, @quialifier, @goid, 
+              @qualifier.join("|"), @evidence, @with.join("|"), @aspect,
+              @db_object_name, @db_object_synonym.join("|"), @db_object_type,
+              @taxon, @date, @assigned_by].join("\t")
+    end
+
+  end # class GeneAssociation   
+
+
+
+  # = Container class for files in geneontology.org/go/external2go/*2go.
+  #
+  # The line syntax is: 
+  #
+  # database:<identifier> > GO:<term> ; GO:<GO_id>
+  #
+  # == Example
+  # 
+  #  spkw2go = Bio::GO::External2go.new(File.read("spkw2go"))
+  #  spkw2go.size
+  #  spkw2go.each do |relation|
+  #    relation # -> {:db => "", :db_id => "", :go_term => "", :go_id => ""}
+  #  end
+  #  spkw2go.dbs
+  #
+  # == SAMPLE
+  #  !date: 2005/02/08 18:02:54
+  #  !Mapping of SWISS-PROT KEYWORDS to GO terms.
+  #  !Evelyn Camon, SWISS-PROT.
+  #  !
+  #  SP_KW:ATP synthesis > GO:ATP biosynthesis ; GO:0006754
+  #  ...
+  #
+  class External2go < Array
+
+    # Returns aHash of the external2go header information
+    attr_reader :header
+
+    # Constructor from parsing external2go file.
+    def self.parser(str)
+      e2g = self.new
+      str.each_line do |line|
+        line.chomp!
+        if line =~ /^\!date: (.+)/
+          e2g.header[:date] = $1
+        elsif line =~ /^\!(.*)/
+          e2g.header[:desc] << $1
+        elsif ary = line.scan(/^(.+?):(.+) > GO:(.+) ; (GO:\d{7})/).first
+          e2g << {:db_id => ary[1], :db => ary[0], :go_term => ary[2], :go_id => ary[3]}
+        else
+          raise("Invalid Format Line: \n #{line.inspect}\n")
+        end
+      end
+      return e2g
+    end
+
+
+    # Constructor.
+    # relation := {:db => aStr, :db_id => aStr, :go_term => aStr, :go_id => aStr}
+    def initialize
+      @header = {:date => '', :desc => []}
+      super
+    end
+
+
+    # Bio::GO::External2go#set_date(value)
+    def set_date(value)
+      @header[:date] = value
+    end
+
+
+    # Bio::GO::External2go#set_desc(ary)
+    def set_desc(ary)
+      @header[:desc] = ary
+    end
+
+
+    # Bio::GO::External2go#to_str
+    # Returns the contents in the external2go format.
+    def to_str
+      ["!date: #{@header[:date]}",
+       @header[:desc].map {|e| "!#{e}" },
+        self.map { |e| [e[:db], ':', e[:db_id], ' > GO:', e[:go_term], ' ; ', e[:go_id]].join }
+      ].join("\n")
+    end
+    
+
+    # Returns ary of databases.
+    def dbs
+      self.map {|rel| rel[:db] }.uniq
+    end
+
+
+    # Returns ary of database IDs.
+    def db_ids
+      self.map {|rel| rel[:db_id] }.uniq
+    end
+
+    # Returns ary of GO Terms.
+    def go_terms
+      self.map {|rel| rel[:go_term] }.uniq
+    end
+
+    # Returns ary of GO IDs.
+    def go_ids
+      self.map {|rel| rel[:go_id] }.uniq
+    end
+
+  end # class External2go
+  
+end # class GO
+
+end # module Bio
+
+
+
+
+
+if __FILE__ == $0
+
+  require 'net/http'
+
+  def wget(url)
+    if /http:\/\/(.+?)\// =~ url
+      host = $1
+      path = url[(url.index(host) + host.size)..url.size]
+    else
+      raise ArgumentError, "Invalid URL\n#{url}"
+    end
+
+    result = Net::HTTP.new(host).get(path).body
+  end
+
+
+
+  go_c_url = 'http://www.geneontology.org/ontology/component.ontology'
+  ga_url = 'http://www.geneontology.org/gene-associations/gene_association.sgd.gz'
+  e2g_url = 'http://www.geneontology.org/external2go/spkw2go'
+
+
+
+  puts "\n #==> Bio::GO::Ontology"
+  p go_c_url
+  component_ontology = wget(go_c_url)
+  comp = Bio::GO::Ontology.new(component_ontology)
+
+  [['0003673', '0005632'],
+    ['0003673', '0005619'],
+    ['0003673', '0004649']].each {|pair|
+    puts
+    p pair
+    p [:pair, pair.map {|i| [comp.id2term[i], comp.goid2term(i)] }]
+    puts "\n #==> comp.bfs_shortest_path(pair[0], pair[1])"
+    p comp.bfs_shortest_path(pair[0], pair[1])
+  }
+
+
+  puts "\n #==> Bio::GO::External2go"
+  p e2g_url
+  spkw2go = Bio::GO::External2go.new(wget(e2g_url))
+
+  puts "\n #==> spkw2go.db"
+  p spkw2go.db
+
+  puts "\n #==> spkw2go[1]"
+  p spkw2go[1]
+
+
+
+  require 'zlib'
+  puts "\n #==> Bio::GO::GeenAssociation"
+  p ga_url
+  ga = Zlib::Inflate.inflate(wget(ga_url))
+  ga = Bio::GO::GeneAssociation.parser(ga)
+
+  puts "\n #==> ga.size"
+  p ga.size
+
+  puts "\n #==> ga[100]"
+  p ga[100]
+
+
+
+
+  
+end