bio 0.7.0

data/lib/bio/db/embl/swissprot.rb

@@ -0,0 +1,32 @@
+#
+# bio/db/embl/swissprot.rb - SwissProt database class
+# 
+#   Copyright (C) 2001, 2002 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: swissprot.rb,v 1.3 2004/08/23 23:40:35 k Exp $
+#
+
+require 'bio/db/embl/sptr'
+
+module Bio
+
+class SwissProt < SPTR
+  # Nothing to do (SwissProt format is abstracted in SPTR)
+end
+
+end
+

data/lib/bio/db/embl/trembl.rb

@@ -0,0 +1,31 @@
+#
+# bio/db/embl/trembl.rb - TrEMBL database class
+# 
+#   Copyright (C) 2001, 2002 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: trembl.rb,v 1.3 2004/08/23 23:40:35 k Exp $
+#
+
+require 'bio/db/embl/sptr'
+
+module Bio
+
+class TrEMBL < SPTR
+  # Nothing to do (TrEMBL format is abstracted in SPTR)
+end
+
+end

data/lib/bio/db/embl/uniprot.rb

@@ -0,0 +1,32 @@
+#
+# bio/db/embl/uniprot.rb - UniProt database class
+# 
+#   Copyright (C) 2005 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: uniprot.rb,v 1.1 2005/09/10 23:43:35 k Exp $
+#
+
+require 'bio/db/embl/sptr'
+
+module Bio
+
+class UniProt < SPTR
+  # Nothing to do (UniProt format is abstracted in SPTR)
+end
+
+end
+

data/lib/bio/db/fantom.rb

@@ -0,0 +1,604 @@
+#
+# bio/db/fantom.rb - RIKEN FANTOM2 database classes
+#
+#   Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+#
+#  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: fantom.rb,v 1.11 2005/09/26 13:00:06 k Exp $
+#
+
+begin
+  require 'rexml/document'
+  rescue LoadError
+end
+require 'uri'
+require 'net/http'
+
+require 'bio/db'
+#require 'bio/sequence'
+
+module Bio
+
+  module FANTOM
+
+    def query(idstr, http_proxy = nil)
+      xml = get_by_id(idstr, http_proxy)
+      seqs = MaXML::Sequences.new(xml.to_s)
+      seqs[0]
+    end
+    module_function :query
+
+    def get_by_id(idstr, http_proxy = nil)
+      addr = 'fantom.gsc.riken.go.jp'
+      port = 80
+      path = "/db/maxml/maxmlseq.cgi?masterid=#{URI.escape(idstr.to_s)}&style=xml"
+      proxy = URI.parse(http_proxy.to_s)
+      xml = ''
+      Net::HTTP.start(addr, port, proxy.host, proxy.port) do |http|
+        response, = http.get(path)
+        xml = response.body
+      end
+      xml
+    end
+    module_function :get_by_id
+
+
+    class MaXML < DB
+      # DTD of MaXML(Mouse annotation XML)
+      # http://fantom.gsc.riken.go.jp/maxml/maxml.dtd
+
+      DELIMITER = RS = "\n--EOF--\n"
+      # This class is for {allseq|repseq|allclust}.sep.xml,
+      # not for {allseq|repseq|allclust}.xml.
+
+      Data_XPath = ''
+
+      def initialize(x)
+        if x.is_a?(REXML::Element) then
+          @elem = x
+        else
+          if x.is_a?(String) then
+            x = x.sub(/#{Regexp.escape(DELIMITER)}\z/om, "\n")
+          end
+          doc = REXML::Document.new(x)
+          @elem = doc.elements[self.class::Data_XPath]
+          #raise 'element is null' unless @elem
+          @elem = REXML::Document.new('') unless @elem
+        end
+      end
+      attr_reader :elem
+
+      def to_s
+        @elem.to_s
+      end
+
+      def gsub_entities(str)
+        # workaround for bug?
+        if str then
+          str.gsub(/\&\#(\d{1,3})\;/) { sprintf("%c", $1.to_i) }
+        else
+          str
+        end
+      end
+
+      def entry_id
+        unless defined?(@entry_id)
+          @entry_id = @elem.attributes['id']
+        end
+        @entry_id
+      end
+      def self.define_element_text_method(array)
+        array.each do |tagstr|
+          module_eval("
+            def #{tagstr}
+              unless defined?(@#{tagstr})
+                @#{tagstr} = gsub_entities(@elem.text('#{tagstr}'))
+              end
+              @#{tagstr}
+            end
+          ")
+        end
+      end
+      private_class_method :define_element_text_method
+
+      class Cluster < MaXML
+        # (MaXML cluster)
+        # ftp://fantom2.gsc.riken.go.jp/fantom/2.1/allclust.sep.xml.gz
+
+        Data_XPath = 'maxml-clusters/cluster'
+
+        def representative_seqid
+          unless defined?(@representative_seqid)
+            @representative_seqid =
+              gsub_entities(@elem.text('representative-seqid'))
+          end
+          @representative_seqid
+        end
+
+        def sequences
+          unless defined?(@sequences)
+            @sequences = MaXML::Sequences.new(@elem)
+          end
+          @sequences
+        end
+
+        def sequence(idstr = nil)
+          idstr ? sequences[idstr] : representative_sequence
+        end
+
+        def representative_sequence
+          unless defined?(@representative_sequence)
+            rid = representative_seqid
+ 	    @representative_sequence =
+              rid ? sequences[representative_seqid] : nil
+          end
+          @representative_sequence
+        end
+        alias representative_clone representative_sequence
+
+        def representative_annotations
+          e = representative_sequence
+          e ? e.annotations : nil
+        end
+
+        def representative_cloneid
+          e = representative_sequence
+          e ? e.cloneid : nil
+        end
+
+        define_element_text_method(%w(fantomid))
+      end #class MaXML::Cluster
+
+      class Sequences < MaXML
+        Data_XPath = 'maxml-sequences'
+
+        include Enumerable
+        def each
+          to_a.each { |x| yield x }
+        end
+
+        def to_a
+          unless defined?(@sequences)
+            @sequences = @elem.get_elements('sequence')
+            @sequences.collect! { |e| MaXML::Sequence.new(e) }
+          end
+          @sequences
+        end
+
+        def get(idstr)
+          unless defined?(@hash)
+            @hash = {}
+          end
+          unless @hash.member?(idstr) then
+            @hash[idstr] = self.find do |x|
+              x.altid.values.index(idstr)
+            end
+          end
+          @hash[idstr]
+        end
+
+        def [](*arg)
+          if arg[0].is_a?(String) and arg.size == 1 then
+            get(arg[0])
+          else
+            to_a[*arg]
+          end
+        end
+
+        def cloneids
+          unless defined?(@cloneids)
+            @cloneids = to_a.collect { |x| x.cloneid }
+          end
+          @cloneids
+        end
+
+        def id_strings
+          unless defined?(@id_strings)
+            @id_strings = to_a.collect { |x| x.id_strings }
+            @id_strings.flatten!
+            @id_strings.sort!
+            @id_strings.uniq!
+          end
+          @id_strings
+        end
+      end #class MaXML::Sequences
+
+      class Sequence < MaXML
+        # (MaXML sequence)
+        # ftp://fantom2.gsc.riken.go.jp/fantom/2.1/allseq.sep.xml.gz
+        # ftp://fantom2.gsc.riken.go.jp/fantom/2.1/repseq.sep.xml.gz
+        
+        Data_XPath = 'maxml-sequences/sequence'
+
+        def altid(t = nil)
+          unless defined?(@altid)
+            @altid = {}
+            @elem.each_element('altid') do |e|
+              @altid[e.attributes['type']] = gsub_entities(e.text)
+            end
+          end
+          if t then
+            @altid[t]
+          else
+            @altid
+          end
+        end
+
+        def id_strings
+          altid.values.sort.uniq
+        end
+
+        def library_id
+          entry_id[0,2]
+        end
+
+        def annotations
+          unless defined?(@annotations)
+            @annotations =
+              MaXML::Annotations.new(@elem.elements['annotations'])
+          end
+          @annotations
+        end
+
+        define_element_text_method(%w(annotator version modified_time comment))
+
+        def self.define_id_method(array)
+          array.each do |tagstr|
+            module_eval("
+              def #{tagstr}
+                unless defined?(@#{tagstr})
+                  @#{tagstr} = gsub_entities(@elem.text('#{tagstr}'))
+                  @#{tagstr} = altid('#{tagstr}') unless @#{tagstr}
+                end
+                @#{tagstr}
+              end
+            ")
+          end
+        end
+        private_class_method :define_id_method
+
+        define_id_method(%w(seqid fantomid cloneid rearrayid accession))
+      end #class MaXML::Sequence
+
+      class Annotations < MaXML
+        Data_XPath = nil
+
+        include Enumerable
+        def each
+          to_a.each { |x| yield x }
+        end
+
+        def to_a
+          unless defined?(@a)
+            @a = @elem.get_elements('annotation')
+            @a.collect! { |e| MaXML::Annotation.new(e) }
+          end
+          @a
+        end
+
+        def get_all_by_qualifier(qstr)
+          unless defined?(@hash)
+            @hash = {}
+          end
+          unless @hash.member?(qstr) then
+            @hash[qstr] = self.find_all do |x|
+              x.qualifier == qstr
+            end
+          end
+          @hash[qstr]
+        end
+
+        def get_by_qualifier(qstr)
+          a = get_all_by_qualifier(qstr)
+          a ? a[0] : nil
+        end
+
+        def [](*arg)
+          if arg[0].is_a?(String) and arg.size == 1 then
+            get_by_qualifier(arg[0])
+          else
+            to_a[*arg]
+          end
+        end
+
+        def cds_start
+          unless defined?(@cds_start)
+            e = get_by_qualifier('cds_start')
+            @cds_start = e ? e.anntext.to_i : nil
+          end
+          @cds_start
+        end
+
+        def cds_stop
+          unless defined?(@cds_stop)
+            e = get_by_qualifier('cds_stop')
+            @cds_stop = e ? e.anntext.to_i : nil
+          end
+          @cds_stop
+        end
+
+        def gene_name
+          unless defined?(@gene_name)
+            e = get_by_qualifier('gene_name')
+            @gene_name = e ? e.anntext : nil
+          end
+          @gene_name
+        end
+
+        def data_source
+          unless defined?(@data_source)
+            e = get_by_qualifier('gene_name')
+            @data_source = e ? e.datasrc[0] : nil
+          end
+          @data_source
+        end
+
+        def evidence
+          unless defined?(@evidence)
+            e = get_by_qualifier('gene_name')
+            @evidence = e ? e.evidence : nil
+          end
+          @evidence
+        end
+      end #class MaXML::Annotations
+
+      class Annotation < MaXML
+        def entry_id
+          nil
+        end
+
+        class DataSrc < String
+          def initialize(text, href)
+            super(text)
+            @href = href
+          end
+          attr_reader :href
+        end
+
+        def datasrc
+          unless defined?(@datasrc)
+            @datasrc = []
+            @elem.each_element('datasrc') do |e|
+              text = e.text
+              href = e.attributes['href']
+              @datasrc << DataSrc.new(gsub_entities(text), gsub_entities(href))
+            end
+          end
+          @datasrc
+        end
+
+        define_element_text_method(%w(qualifier srckey anntext evidence))
+      end #class MaXML::Annotation
+
+    end #class MaXML
+
+  end #module FANTOM
+
+end #module Bio
+
+=begin
+
+ Bio::FANTOM are database classes (and modules) treating RIKEN FANTOM2 data.
+ FANTOM2 is available at ((<URL:http://fantom2.gsc.riken.go.jp/>)).
+
+= Bio::FANTOM
+
+ This module contains useful methods to access databases.
+
+--- Bio::FANTOM.query(idstr, http_proxy=nil)
+
+ Get MaXML sequence data corresponding to given ID through the internet
+ from ((<URL:http://fantom.gsc.riken.go.jp/db/maxml/)).
+ Returns Bio::FANTOM::MaXML::Sequence object.
+
+--- Bio::FANTOM.get_by_id(idstr, http_proxy=nil)
+
+ Same as FANTOM.query, but returns XML document as a string.
+ (Reference: bio/io/registry.rb)
+
+
+= Bio::FANTOM::MaXML::Cluster
+
+ This class is for 'allclust.sep.xml' found at
+ ((<URL:ftp://fantom2.gsc.riken.go.jp/fantom/2.1/allclust.sep.xml.gz>)).
+ Not that this class is not suitable for 'allclust.xml'.
+
+--- Bio::FANTOM::MaXML::Cluster.new(str)
+
+--- Bio::FANTOM::MaXML::Cluster#entry_id
+
+--- Bio::FANTOM::MaXML::Cluster#fantomid
+
+--- Bio::FANTOM::MaXML::Cluster#representative_seqid
+
+--- Bio::FANTOM::MaXML::Cluster#sequences
+
+ Lists sequences in this cluster.
+ Returns Bio::FANTOM::MaXML::Sequences object.
+
+--- Bio::FANTOM::MaXML::Cluster#sequence(id_str)
+
+ Shows a sequence information of given id.
+ Returns Bio::FANTOM::MaXML::Sequence object or nil.
+
+--- Bio::FANTOM::MaXML::Cluster#representataive_sequence
+--- Bio::FANTOM::MaXML::Cluster#representataive_clone
+
+ Shows a sequence of repesentative_seqid.
+ Returns Bio::FANTOM::MaXML::Sequence object (or nil).
+
+-- Bio::FANTOM::MaXML::Cluster#representative_annotations
+
+ Shows annotations of repesentative sequence.
+ Returns Bio::FANTOM::MaXML::Annotations object (or nil).
+
+-- Bio::FANTOM::MaXML::Cluster#representative_cloneid
+
+ Shows cloneid of repesentative sequence.
+ Returns String (or nil).
+
+
+= Bio::FANTOM::MaXML::Sequences
+
+ The instances of this class are automatically created
+ by Bio::FANTOM::MaXML::Cluster class.
+
+ This class can also be used for 'allseq.sep.xml' and 'repseq.sep.xml',
+ but you'd better using Bio::FANTOM::MaXML::Sequence class.
+
+ In addition, this class can be used for 'allseq.xml' and 'repseq.xml',
+ but you'd better not to use them, becase of the speed is very slow.
+
+--- Bio::FANTOM::MaXML::Sequences#to_a
+
+ Returns an Array of Bio::FANTOM::MaXML::Sequence objects.
+
+--- Bio::FANTOM::MaXML::Sequences#each
+
+--- Bio::FANTOM::MaXML::Sequences#[](x)
+
+ Same as to_a[x] when x is a integer.
+ Same as get[x] when x is a string.
+
+--- Bio::FANTOM::MaXML::Sequences#get(id_str)
+
+ Shows a sequence information of given id.
+ Returns Bio::FANTOM::MaXML::Sequence object or nil.
+
+--- Bio::FANTOM::MaXML::Sequences#cloneids
+
+ Shows clone ID list.
+ Returns an array of strings.
+
+--- Bio::FANTOM::MaXML::Sequences#id_strings
+
+ Shows ID list.
+ Returns an array of strings.
+
+
+= Bio::FANTOM::MaXML::Sequence
+
+ This class is for 'allseq.sep.xml' and 'repseq.sep.xml' found at
+ ((<URL:ftp://fantom2.gsc.riken.go.jp/fantom/2.1/allseq.sep.xml.gz>)) and
+ ((<URL:ftp://fantom2.gsc.riken.go.jp/fantom/2.1/repseq.sep.xml.gz>)).
+ Not that this class is not suitable for 'allseq.xml' and 'repseq.xml'.
+
+ In addition, the instances of this class are automatically created
+ by Bio::FANTOM::MaXML::Sequences class.
+
+--- Bio::FANTOM::MaXML::Sequence.new(str)
+
+--- Bio::FANTOM::MaXML::Sequence#entry_id
+
+--- Bio::FANTOM::MaXML::Sequence#altid(type_str = nil)
+
+ Returns hash of altid if no arguments are given.
+ Returns ID as a string if a type of ID (string) is given.
+
+--- Bio::FANTOM::MaXML::Sequence#annotations
+
+ Gets lists of annotation data.
+ Returns a Bio::FANTOM::MaXML::Annotations object.
+
+--- Bio::FANTOM::MaXML::Sequence#id_strings
+
+ Gets lists of ID. (same as altid.values)
+ Returns an array of strings.
+
+--- Bio::FANTOM::MaXML::Sequence#library_id
+
+ Shows library ID. (same as cloneid[0,2])
+ Library IDs are listed at:
+   ((<URL:http://fantom2.gsc.riken.go.jp/fantom2/SI/sup01_est_3r_libraryinfo.pdf))
+   ((<URL:http://fantom2.gsc.riken.go.jp/fantom2/SI/sup01_est_5f_libraryinfo.pdf))
+
+--- Bio::FANTOM::MaXML::Sequence#seqid
+
+--- Bio::FANTOM::MaXML::Sequence#fantomid
+
+--- Bio::FANTOM::MaXML::Sequence#cloneid
+
+--- Bio::FANTOM::MaXML::Sequence#rearrayid
+
+--- Bio::FANTOM::MaXML::Sequence#accession
+
+--- Bio::FANTOM::MaXML::Sequence#annotator
+
+--- Bio::FANTOM::MaXML::Sequence#version
+
+--- Bio::FANTOM::MaXML::Sequence#modified_time
+
+--- Bio::FANTOM::MaXML::Sequence#comment
+
+
+= Bio::FANTOM::MaXML::Annotations
+
+ The instances of this class are automatically created
+ by Bio::FANTOM::MaXML::Sequence class.
+
+--- Bio::FANTOM::MaXML::Annotations#to_a
+
+ Returns an Array of Bio::FANTOM::MaXML::Annotations objects.
+
+--- Bio::FANTOM::MaXML::Annotations#each
+
+--- Bio::FANTOM::MaXML::Annotations#get_all_by_qualifier(qstr)
+
+--- Bio::FANTOM::MaXML::Annotations#get_by_qualifier(qstr)
+
+--- Bio::FANTOM::MaXML::Annotations#[](x)
+
+ Same as to_a[x] when x is a integer.
+ Same as get_by_qualifier[x] when x is a string.
+
+--- Bio::FANTOM::MaXML::Annotations#cds_start
+--- Bio::FANTOM::MaXML::Annotations#cds_stop
+--- Bio::FANTOM::MaXML::Annotations#gene_name
+--- Bio::FANTOM::MaXML::Annotations#data_source
+--- Bio::FANTOM::MaXML::Annotations#evidence
+
+
+= Bio::FANTOM::MaXML::Annotation
+
+ The instances of this class are automatically created
+ by Bio::FANTOM::MaXML::Annotations class.
+
+--- Bio::FANTOM::MaXML::Annotation#datasrc
+
+ Returns an Array of Bio::FANTOM::MaXML::Annotation::DataSrc objects.
+
+--- Bio::FANTOM::MaXML::Annotation#qualifier
+
+--- Bio::FANTOM::MaXML::Annotation#srckey
+
+--- Bio::FANTOM::MaXML::Annotation#anntext
+
+--- Bio::FANTOM::MaXML::Annotation#evidence
+
+= Bio::FANTOM::MaXML::Annotation::DataSrc < String
+
+ The instances of this class are automatically created
+ by Bio::FANTOM::MaXML::Annotation class.
+
+---- Bio::FANTOM::MaXML::Annotation::DataSrc#href
+
+ Shows a link URL to database web page as an String.
+
+= References
+
+* ((<URL:http://fantom2.gsc.riken.go.jp/>))
+
+=end