bio 1.2.1 → 1.3.0

data/lib/bio/io/hinv.rb

@@ -0,0 +1,442 @@
+#
+# = bio/io/hinv.rb - H-invDB web service (REST) client module
+#
+# Copyright::  Copyright (C) 2008 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# $Id:$
+#
+
+require 'bio/command'
+require 'rexml/document'
+
+module Bio
+
+  # = Bio::Hinv
+  #
+  # Accessing the H-invDB web services.
+  #
+  # * http://www.h-invitational.jp/
+  # * http://www.jbirc.aist.go.jp/hinv/hws/doc/index.html
+  #
+  class Hinv
+
+    BASE_URI = "http://www.jbirc.aist.go.jp/hinv/hws/"
+
+    module Common
+      def query(options = nil)
+        response = Bio::Command.post_form(@url, options)
+        @result = response.body
+        @xml = REXML::Document.new(@result)
+      end
+    end
+
+
+    # Bio::Hinv.acc2hit("BC053657")  # => "HIT000053961"
+    def self.acc2hit(acc)
+      serv = Acc2hit.new
+      serv.query("acc" => acc)
+      serv.result
+    end
+
+    # Bio::Hinv.hit2acc("HIT000022181")  # => "AK097327"
+    def self.hit2acc(hit)
+      serv = Hit2acc.new
+      serv.query("hit" => hit)
+      serv.result
+    end
+
+    # Bio::Hinv.hit_cnt  # => 187156
+    def self.hit_cnt
+      serv = HitCnt.new
+      serv.query
+      serv.result
+    end
+
+    # Bio::Hinv.hit_definition("HIT000000001")  # => "Rho guanine ..."
+    def self.hit_definition(hit)
+      serv = HitDefinition.new
+      serv.query("hit" => hit)
+      serv.result
+    end
+
+    # Bio::Hinv.hit_pubmedid("HIT000053961")  # => [7624364, 11279095, ... ]
+    def self.hit_pubmedid(hit)
+      serv = HitPubmedId.new
+      serv.query("hit" => hit)
+      serv.result
+    end
+
+    # Bio::Hinv.hit_xml("HIT000000001")  # => "<?xml version="1.0" ..."
+    def self.hit_xml(hit)
+      serv = Bio::Hinv::HitXML.new
+      serv.query("hit" => hit)
+      puts serv.result
+    end
+
+    # Bio::Hinv.hix2hit("HIX0000004")  # => ["HIT000012846", ... ]
+    def self.hix2hit(hix)
+      serv = Bio::Hinv::Hix2hit.new
+      serv.query("hix" => hix)
+      serv.result
+    end
+
+    # Bio::Hinv.hix_cnt  # => 36073
+    def self.hix_cnt
+      serv = HixCnt.new
+      serv.query
+      serv.result
+    end
+
+    # Bio::Hinv.hix_represent("HIX0000001")  # => "HIT000022181"
+    def self.hix_represent(hix)
+      serv = HixRepresent.new
+      serv.query("hix" => hix)
+      serv.result
+    end
+
+    # Bio::Hinv.id_search("HIT00002218*")  # => ["HIT000022181", ... ]
+    def self.id_search(query)
+      serv = IdSearch.new
+      serv.query("query" => query)
+      serv.result
+    end
+
+    # Bio::Hinv.keyword_search("HIT00002218*")  # => ["HIT000022181", ... ]
+    def self.keyword_search(query)
+      serv = KeywordSearch.new
+      serv.query("query" => query)
+      serv.result
+    end
+
+
+    # serv = Bio::Hinv::Acc2hit.new
+    # serv.query("acc" => "BC053657")
+    # puts serv.result
+    class Acc2hit
+      include Common
+
+      def initialize
+        @url = BASE_URI + "acc2hit.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <H-INVITATIONAL-ID>HIT000053961</H-INVITATIONAL-ID>
+      # </H-Inv>
+      def result
+        @xml.elements['//H-INVITATIONAL-ID'].text
+      end
+    end
+
+    # serv = Bio::Hinv::Hit2acc.new
+    # serv.query("hit" => "HIT000022181")
+    # puts serv.result
+    class Hit2acc
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit2acc.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <ACCESSION-NO>AK097327</ACCESSION-NO>
+      # </H-Inv>
+      def result
+        @xml.elements['//ACCESSION-NO'].text
+      end
+    end
+
+    # serv = Bio::Hinv::HitCnt.new
+    # serv.query
+    # puts serv.result
+    class HitCnt
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit_cnt.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <TRANSCRIPT_CNT>187156</TRANSCRIPT_CNT>
+      # </H-Inv>
+      def result
+        @xml.elements['//TRANSCRIPT_CNT'].text.to_i
+      end
+    end
+
+    # serv = Bio::Hinv::HitDefinition.new
+    # serv.query("hit" => "HIT000000001")
+    # puts serv.result
+    # puts serv.data_source_definition
+    # puts serv.cdna_rep_h_invitational
+    # puts serv.cdna_splicing_isoform_curation
+    # puts serv.data_source_db_reference_protein_motif_id
+    # puts serv.data_source_identity
+    # puts serv.data_source_coverage
+    # puts serv.data_source_homologous_species
+    # puts serv.data_source_similarity_category
+    class HitDefinition
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit_definition.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <HIT_FUNCTION>
+      #   <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
+      #   <DATA-SOURCE_DEFINITION>Rho guanine nucleotide exchange factor 10.</DATA-SOURCE_DEFINITION>
+      #   <CDNA_REP-H-INVITATIONAL>Representative transcript</CDNA_REP-H-INVITATIONAL>
+      #   <CDNA_SPLICING-ISOFORM_CURATION></CDNA_SPLICING-ISOFORM_CURATION>
+      #   <DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>NP_055444</DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>
+      #   <DATA-SOURCE_IDENTITY>100.0</DATA-SOURCE_IDENTITY>
+      #   <DATA-SOURCE_COVERAGE>100.0</DATA-SOURCE_COVERAGE>
+      #   <DATA-SOURCE_HOMOLOGOUS_SPECIES>Homo sapiens</DATA-SOURCE_HOMOLOGOUS_SPECIES>
+      #   <DATA-SOURCE_SIMILARITY-CATEGORY>Identical to known human protein(Category I).</DATA-SOURCE_SIMILARITY-CATEGORY>
+      #  </HIT_FUNCTION>
+      # </H-Inv>
+      def result
+        @xml.elements['//DATA-SOURCE_DEFINITION'].text
+      end
+      alias :data_source_definition :result
+
+      def cdna_rep_h_invitational
+        @xml.elements['//CDNA_REP-H-INVITATIONAL'].text
+      end
+      def cdna_splicing_isoform_curation
+        @xml.elements['//CDNA_SPLICING-ISOFORM_CURATION'].text
+      end
+      def data_source_db_reference_protein_motif_id
+        @xml.elements['//DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID'].text
+      end
+      def data_source_identity
+        @xml.elements['//DATA-SOURCE_IDENTITY'].text.to_f
+      end
+      def data_source_coverage
+        @xml.elements['//DATA-SOURCE_COVERAGE'].text.to_f
+      end
+      def data_source_homologous_species
+        @xml.elements['//DATA-SOURCE_HOMOLOGOUS_SPECIES'].text
+      end
+      def data_source_similarity_category
+        @xml.elements['//DATA-SOURCE_SIMILARITY-CATEGORY'].text
+      end
+    end
+
+    # serv = Bio::Hinv::HitPubmedId.new
+    # serv.query("hit" => "HIT000053961")
+    # puts serv.result
+    class HitPubmedId
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit_pubmedid.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <CDNA_DB-REFERENCE_PUBMED>7624364</CDNA_DB-REFERENCE_PUBMED>
+      #  <CDNA_DB-REFERENCE_PUBMED>11279095</CDNA_DB-REFERENCE_PUBMED>
+      #  <CDNA_DB-REFERENCE_PUBMED>15489334</CDNA_DB-REFERENCE_PUBMED>
+      # </H-Inv>
+      def result
+        list = []
+        @xml.elements.each('//CDNA_DB-REFERENCE_PUBMED') do |e|
+          list << e.text.to_i
+        end
+        return list
+      end
+    end
+
+    # serv = Bio::Hinv::HitXML.new
+    # serv.query("hit" => "HIT000000001")
+    # puts serv.result
+    class HitXML
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit_xml.php"
+      end
+
+      # <?xml version="1.0" standalone="yes" ?>
+      # <H-Inv>
+      #  <cDNAXML>
+      #  <CLUSTER-ID>HIX0021591</CLUSTER-ID>
+      #  <CLUSTER-ID-VERSION>HIX0021591.11</CLUSTER-ID-VERSION>
+      #  <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
+      #    :
+      #    </PROBE-MAPPING>
+      #   </EXPRESSION>
+      #  </cDNAXML>
+      # </H-Inv>
+      def result
+        @result
+      end
+    end
+
+    # serv = Bio::Hinv::Hix2hit.new
+    # serv.query("hix" => "HIX0000004")
+    # puts serv.result
+    class Hix2hit
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hix2hit.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <H-INVITATIONAL-ID>HIT000012846</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022124</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000007722</H-INVITATIONAL-ID>
+      #    :
+      #  <H-INVITATIONAL-ID>HIT000262478</H-INVITATIONAL-ID>
+      # </H-Inv>
+      def result
+        list = []
+        @xml.elements.each('//H-INVITATIONAL-ID') do |e|
+          list << e.text
+        end
+        return list
+      end
+    end
+
+    # serv = Bio::Hinv::HixCnt.new
+    # serv.query
+    # puts serv.result
+    class HixCnt
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hix_cnt.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <LOCUS_CNT>36073</LOCUS_CNT>
+      # </H-Inv>
+      def result
+        @xml.elements['//LOCUS_CNT'].text.to_i
+      end
+    end
+
+    # serv = Bio::Hinv::HixRepresent.new
+    # serv.query("hix" => "HIX0000001")
+    # puts serv.result
+    # puts serv.rep_h_invitational_id
+    # puts serv.rep_accession_no
+    class HixRepresent
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hix_represent.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <LOCUS>
+      #   <CLUSTER-ID>HIX0000001</CLUSTER-ID>
+      #   <REP-H-INVITATIONAL-ID>HIT000022181</REP-H-INVITATIONAL-ID>
+      #   <REP-ACCESSION-NO>AK097327</REP-ACCESSION-NO>
+      #  </LOCUS>
+      # </H-Inv>
+      def result
+        @xml.elements['//REP-H-INVITATIONAL-ID'].text
+      end
+      alias :rep_h_invitational_id :result
+
+      def rep_accession_no
+        @xml.elements['//REP-ACCESSION-NO'].text
+      end
+    end
+
+    # example at "http://www.jbirc.aist.go.jp/hinv/hws/doc/index_jp.html"
+    # is for hit_xml.php (not for hix_xml.php)
+    class HixXML
+    end
+
+    # serv = Bio::Hinv::KeywordSearch.new
+    # serv.query("query" => "HIT00002218*", "start" => 1, "end" => 100)
+    # puts serv.result
+    # puts serv.size
+    # puts serv.start
+    # puts serv.end
+    class KeywordSearch
+      include Common
+
+      def initialize
+        @url = BASE_URI + "keyword_search.php"
+      end
+
+      def query(hash = {})
+        default = {
+          "start" => 1,
+          "end" => 100
+        }
+        options = default.update(hash)
+        super(options)
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <HINVDB_SEARCH>
+      #  <QUERY>HIT00002218*</QUERY>
+      #  <SIZE>8</SIZE>
+      #  <START>1</START>
+      #  <END>8</END>
+      #  <H-INVITATIONAL-ID>HIT000022180</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022181</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022183</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022184</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022185</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022186</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022188</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022189</H-INVITATIONAL-ID>
+      # </HINVDB_SEARCH>
+      def result
+        list = []
+        @xml.elements.each('//H-INVITATIONAL-ID') do |e|
+          list << e.text
+        end
+        return list
+      end
+
+      def size
+        @xml.elements['//SIZE'].text.to_i
+      end
+      def start
+        @xml.elements['//START'].text.to_i
+      end
+      def end
+        @xml.elements['//END'].text.to_i
+      end
+    end
+
+    # serv = Bio::Hinv::IdSearch.new
+    # serv.query("query" => "HIT00002218*", "id_type" => "H-INVITATIONAL-ID", "start" => 1, "end" => 100)
+    # puts serv.result
+    # puts serv.size
+    # puts serv.start
+    # puts serv.end
+    class IdSearch < KeywordSearch
+      def initialize
+        @url = BASE_URI + "id_search.php"
+      end
+
+      def query(hash = {})
+        default = {
+          "id_type" => "H-INVITATIONAL-ID",
+          "start" => 1,
+          "end" => 100
+        }
+        options = default.update(hash)
+        super(options)
+      end
+    end
+
+  end
+end
+

data/lib/bio/io/keggapi.rb

@@ -4,7 +4,7 @@
 # Copyright::  Copyright (C) 2003, 2004 Toshiaki Katayama <k@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: keggapi.rb,v 1.15 2007/07/20 21:56:45 k Exp $
+# $Id:$
 #
 
 require 'bio/io/soapwsdl'
@@ -269,7 +269,7 @@ class API < Bio::SOAPWSDL
     filename ||= File.basename(path)
 
     http = Bio::Command.new_http(host, port)
-    response, = http.get(path)
+    response = http.get(path)
     File.open(filename, "w+") do |f|
       f.print response.body
     end